2QAD - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF TYROSINE-SULFATED 412D ANTIBODY COMPLEXED WITH HIV-1 YU2 GP120 AND CD4

Authors :   C. -C. Huang, M. Tang, J. Robinson, R. Wyatt, P. D. Kwong

Date :   14 Jun 07 (Deposition) - 25 Sep 07 (Release) - 29 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E,F,G,H  (1x)
Biol. Unit 3: A,B,C,D,E,F,G,H  (1x)

Keywords :   Viral Protein/Immune System, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. -C. Huang, S. N. Lam, P. Acharya, M. Tang, S. -H. Xiang, S. S. Hussan, R. L. Stanfield, J. Robinson, J. Sodroski, I. A. Wilson, R. Wyatt, C. A. Bewley, P. D. Kwong
Structures Of The Ccr5 N Terminus And Of A Tyrosine-Sulfate Antibody With Hiv-1 Gp120 And Cd4
Science V. 317 1930 2007
PubMed-ID: 17901336 | Reference-DOI: 10.1126/SCIENCE.1145373

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
	Chains	:	A, E
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	EMBRYONIC CELL LINE 293
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	CMVR
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	CORE WITH V3
	Gene	:	ENV
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Strain	:	YU2
	Synonym	:	ENV POLYPROTEIN

Molecule 2 - T-CELL SURFACE GLYCOPROTEIN CD4
	Chains	:	B, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS
	Gene	:	CD4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	T-CELL SURFACE ANTIGEN T4/LEU-3

Molecule 3 - ANTI-HIV-1 ANTIBODY 412D LIGHT CHAIN
	Chains	:	C, G
	Engineered	:	YES
	Expression System	:	HUMAN HERPESVIRUS 4
	Expression System Common	:	EPSTEIN-BARR VIRUS
	Expression System Strain	:	EPSTEIN-BARR VIRUS
	Expression System Taxid	:	10376
	Fragment	:	FAB, ANTIGEN-BINDING FRAGMENT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - ANTI-HIV-1 ANTIBODY 412D HEAVY CHAIN
	Chains	:	D, H
	Engineered	:	YES
	Expression System	:	HUMAN HERPESVIRUS 4
	Expression System Common	:	EPSTEIN-BARR VIRUS
	Expression System Strain	:	EPSTEIN-BARR VIRUS
	Expression System Taxid	:	10376
	Fragment	:	FAB, ANTIGEN-BINDING FRAGMENT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H
Biological Unit 3 (1x)	:	A	B	C	D	E	F	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 46)

No.	Name	Count	Type	Full Name
1	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
2	MLA	4	Ligand/Ion	MALONIC ACID
3	NAG	31	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	TYS	4	Mod. Amino Acid	O-SULFO-L-TYROSINE

Biological Unit 1 (4, 24)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	MLA	2	Ligand/Ion	MALONIC ACID
3	NAG	16	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	TYS	2	Mod. Amino Acid	O-SULFO-L-TYROSINE

Biological Unit 2 (4, 22)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	MLA	2	Ligand/Ion	MALONIC ACID
3	NAG	15	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	TYS	2	Mod. Amino Acid	O-SULFO-L-TYROSINE

Biological Unit 3 (4, 46)

No.	Name	Count	Type	Full Name
1	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
2	MLA	4	Ligand/Ion	MALONIC ACID
3	NAG	31	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	TYS	4	Mod. Amino Acid	O-SULFO-L-TYROSINE

Asymmetric Unit (37, 37)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:234 , THR A:236	BINDING SITE FOR RESIDUE NAG A 734
02	AC2	SOFTWARE	ASN A:241	BINDING SITE FOR RESIDUE NAG A 741
03	AC3	SOFTWARE	PRO A:212 , ARG A:252 , LEU A:261 , ASN A:262 , ASN A:377 , CYS A:445 , SER A:447	BINDING SITE FOR RESIDUE NAG A 762
04	AC4	SOFTWARE	ASN A:276 , ASN A:279	BINDING SITE FOR RESIDUE NAG A 776
05	AC5	SOFTWARE	GLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , LYS C:126	BINDING SITE FOR RESIDUE NAG A 789
06	AC6	SOFTWARE	ASN A:295 , ARG A:444 , SER A:446 , NAG E:795 , NAG E:832 , NAG E:913	BINDING SITE FOR RESIDUE NAG A 795
07	AC7	SOFTWARE	ASN A:301	BINDING SITE FOR RESIDUE NAG A 801
08	AC8	SOFTWARE	THR A:297 , HIS A:330 , ASN A:332 , ASN A:413 , NAG A:913	BINDING SITE FOR RESIDUE NAG A 832
09	AC9	SOFTWARE	ASN A:356	BINDING SITE FOR RESIDUE NAG A 856
10	BC1	SOFTWARE	ASN A:362 , PRO A:363 , SER A:364 , SER A:365 , ARG A:469	BINDING SITE FOR RESIDUE NAG A 862
11	BC2	SOFTWARE	ASN A:386 , THR A:388 , GLN A:389	BINDING SITE FOR RESIDUE NAG A 886
12	BC3	SOFTWARE	ILE A:360 , PHE A:361 , ASN A:362 , ASN A:394 , ARG A:397	BINDING SITE FOR RESIDUE NAG A 894
13	BC4	SOFTWARE	ASN A:400 , ASP C:151 , ASN C:152 , LEU C:191	BINDING SITE FOR RESIDUE NAG A 900
14	BC5	SOFTWARE	SER A:334 , ARG A:412 , ASN A:413 , NAG A:832 , NAG E:795	BINDING SITE FOR RESIDUE NAG A 913
15	BC6	SOFTWARE	SER A:291 , ASN A:448	BINDING SITE FOR RESIDUE NAG A 948
16	BC7	SOFTWARE	ASN A:463	BINDING SITE FOR RESIDUE NAG A 963
17	BC8	SOFTWARE	ASN E:234	BINDING SITE FOR RESIDUE NAG E 734
18	BC9	SOFTWARE	ASP E:230 , ASN E:241	BINDING SITE FOR RESIDUE NAG E 741
19	CC1	SOFTWARE	PRO E:212 , VAL E:254 , ASN E:262 , ASN E:377 , CYS E:445 , SER E:446 , SER E:447	BINDING SITE FOR RESIDUE NAG E 762
20	CC2	SOFTWARE	GLU E:275 , ASN E:276	BINDING SITE FOR RESIDUE NAG E 776
21	CC3	SOFTWARE	VAL C:205 , GLU E:268 , GLU E:269 , ASN E:289 , GLU E:290 , GLN E:344	BINDING SITE FOR RESIDUE NAG E 789
22	CC4	SOFTWARE	NAG A:795 , NAG A:913 , ASN E:295 , ARG E:444	BINDING SITE FOR RESIDUE NAG E 795
23	CC5	SOFTWARE	ASN E:301	BINDING SITE FOR RESIDUE NAG E 801
24	CC6	SOFTWARE	NAG A:795 , ASN E:295 , ASN E:332 , THR E:415	BINDING SITE FOR RESIDUE NAG E 832
25	CC7	SOFTWARE	ASN E:356 , GLN H:192 , TYR H:194	BINDING SITE FOR RESIDUE NAG E 856
26	CC8	SOFTWARE	ASN E:362 , PRO E:363 , SER E:364 , NAG E:894	BINDING SITE FOR RESIDUE NAG E 862
27	CC9	SOFTWARE	THR E:240 , VAL E:242 , ASN E:386 , THR E:388	BINDING SITE FOR RESIDUE NAG E 886
28	DC1	SOFTWARE	ASN E:394 , NAG E:862	BINDING SITE FOR RESIDUE NAG E 894
29	DC2	SOFTWARE	NAG A:795 , ASN E:413	BINDING SITE FOR RESIDUE NAG E 913
30	DC3	SOFTWARE	ASN E:262 , SER E:291 , ASN E:448	BINDING SITE FOR RESIDUE NAG E 948
31	DC4	SOFTWARE	ASN E:463 , HIS G:198 , SER G:202	BINDING SITE FOR RESIDUE NAG E 963
32	DC5	SOFTWARE	ARG H:38 , ARG H:62 , GLU H:85 , ASP H:86	BINDING SITE FOR RESIDUE MLA H 215
33	DC6	SOFTWARE	LYS B:2 , VAL B:3 , LYS B:166	BINDING SITE FOR RESIDUE MLA B 186
34	DC7	SOFTWARE	SER F:104	BINDING SITE FOR RESIDUE MLA F 186
35	DC8	SOFTWARE	LYS E:421 , ILE E:491 , GLU E:492	BINDING SITE FOR RESIDUE EDO E 7
36	DC9	SOFTWARE	LYS A:350 , ASN A:355 , ASN A:356 , LYS A:357 , THR A:358	BINDING SITE FOR RESIDUE EDO A 8
37	EC1	SOFTWARE	GLN C:27 , SER C:28	BINDING SITE FOR RESIDUE EDO C 216

Asymmetric Unit

No.	Residues
1	A:119	-	A:205
2	A:218	-	A:247
3	A:228	-	A:239
4	A:296	-	A:331
5	A:378	-	A:445
6	A:385	-	A:418
7	B:16	-	B:84
8	B:130	-	B:159
9	C:23	-	C:88
10	C:134	-	C:194
11	D:22	-	D:92
12	D:140	-	D:196
13	E:119	-	E:205
14	E:218	-	E:247
15	E:228	-	E:239
16	E:296	-	E:331
17	E:378	-	E:445
18	E:385	-	E:418
19	F:16	-	F:84
20	F:130	-	F:159
21	G:23	-	G:88
22	G:134	-	G:194
23	H:22	-	H:92
24	H:140	-	H:196

Asymmetric Unit

No.	Residues
1	Ser C:7	-	Pro C:8
2	Ser C:94	-	Pro C:95
3	Tyr C:140	-	Pro C:141
4	Phe D:146	-	Pro D:147
5	Glu D:148	-	Pro D:149
6	Ser G:7	-	Pro G:8
7	Ser G:94	-	Pro G:95
8	Tyr G:140	-	Pro G:141
9	Phe H:146	-	Pro H:147
10	Glu H:148	-	Pro H:149

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_023459	K	191	E	CD4_HUMAN	Polymorphism	28917504	B/F	K	166	E

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_023459	K	191	E	CD4_HUMAN	Polymorphism	28917504	B	K	166	E

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_023459	K	191	E	CD4_HUMAN	Polymorphism	28917504	F	K	166	E

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_023459	K	191	E	CD4_HUMAN	Polymorphism	28917504	B/F	K	166	E

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2QAD)

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000011653	1	ENSE00001303311	chr12:6898651-6898828	178	CD4_HUMAN	-	0	0	-	-
1.2	ENST00000011653	2	ENSE00000866954	chr12:6909238-6909353	116	CD4_HUMAN	1-17	17	0	-	-
1.3	ENST00000011653	3	ENSE00000716042	chr12:6909473-6909637	165	CD4_HUMAN	17-72	56	2	B:1-47 F:1-47	47 47
1.4	ENST00000011653	4	ENSE00000716044	chr12:6923308-6923466	159	CD4_HUMAN	72-125	54	2	B:47-100 F:47-100	54 54
1.5	ENST00000011653	5	ENSE00000716046	chr12:6923925-6924158	234	CD4_HUMAN	125-203	79	2	B:100-178 F:100-178	79 79
1.6b	ENST00000011653	6b	ENSE00000716048	chr12:6925222-6925569	348	CD4_HUMAN	203-319	117	2	B:178-178 F:178-179	1 2
1.7	ENST00000011653	7	ENSE00000716051	chr12:6926296-6926496	201	CD4_HUMAN	319-386	68	0	-	-
1.8	ENST00000011653	8	ENSE00000716053	chr12:6927587-6927708	122	CD4_HUMAN	386-426	41	0	-	-
1.9	ENST00000011653	9	ENSE00000716057	chr12:6928013-6928080	68	CD4_HUMAN	427-449	23	0	-	-
1.10	ENST00000011653	10	ENSE00001182623	chr12:6928465-6929976	1512	CD4_HUMAN	449-458	10	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:319
 aligned with ENV_HV1Y2 | P35961 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:391
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478 
           ENV_HV1Y2     89 TENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTTSSSWETMEKGEIKNCSFNITTSIRDKVQKEYALFYNLDVVPIDNASYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  479
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh......eee...----------------------------------------------------------------------.eee............eee.....eeeeee.............eeee.............eee.........eeee.........eeeeeeeeeeeeeee....ee..eee..........ee.....eeeeeeehhhhhhhhhhhhhhhhhhhh....eee......hhhhhheeeee..eeeee............--.....eeeeeee...eee......eee........eeeeeeeeeeeeee.........eeeee...hhhhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qad A   90 TENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGG----------------------------------------------------------------------SVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTR--NNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    99       109       119     |   -         -         -         -         -         -         -      |202       212       222       232       242       252       262       272       282       292       302      |314       323       333       343       353       363       373       383       393   |  |403|      421       431       441       451       461       471       481       491 
                                                             125                                                                    199                                                                                                           309|       322A                                                                        397  |  ||                                                                                
                                                                                                                                                                                                                                                   312                                                                                      400  ||                                                                                
                                                                                                                                                                                                                                                                                                                                               403|                                                                                
                                                                                                                                                                                                                                                                                                                                                412

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with CD4_HUMAN | P01730 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:178
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195        
           CD4_HUMAN     26 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLA  203
               SCOP domains d2qadb1 B:1-97 CD4 V-set domains                                                                 d2qadb2 B:98-178 CD4 C2-set domains                                               SCOP domains
               CATH domains 2qadB01 B:1-98 Immunoglobulins                                                                    2qadB02 B:99-173 Immunoglobulins                                           ----- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eee............eee.....eeee...................hhhhhhhh...eee.........eee........eeeeeeeeeee....ee.....eeeeee.........ee.......ee...eeee...hhhhheee..eee....eee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------E------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:1-47 UniProt: 17-72           ----------------------------------------------------Exon 1.5  PDB: B:100-178 UniProt: 125-203                                       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.4  PDB: B:47-100 UniProt: 72-125               -----------------------------------------------------------------------------1 Transcript 1 (2)
                2qad B    1 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLA  178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qadC01 C:1-108 Immunoglobulins                                                                             -2qadC02 C:110-211 Immunoglobulins                                                                     -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeee.....eeeeee.........eeeee......eeeee...ee.......eeeeee..eeeeee.........eeeee............eeeee........eeee..hhhhhh..ee..eeeeeee.................................eee.....eehhhhhh......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qad C    1 DIQMTQSPSTLSASVGDRVTITCRASQSISNWLAWYQQKPGRAPKLLMYKASSLKSGVPSRFSGSGSGTEFTLTISSLQSDDFATYYCQQHDSSPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKLYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain D from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                        
               SCOP domains d2qadd1 D:1-113 Immunoglobulin heavy chain variable domain, VH                                                                    d2qadd2 D:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 2qadD01 D:1-109 Immunoglobulins                                                                                               2qadD02 D:110-214 Immunoglobulins                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.....eee.eee...hhhhh..eeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeee...........................eeee..........................eee...........eee.........ee...ee.....ee..eee.............eee.hhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qad D    1 EVQLVQSGAEVKKPGSSVKVSCKASGGTFSNYAINWVRQAPGQGLEWMGGIIPIFNIAHYAQRFQGRVSITADESTSTAYMELSSLRSEDTAVFYCASPYPNDyNDyAPEEGMSWYFDLWGRGTLVTVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96   |||100F|||||||103       113       123       133       143       153       163       173       183       193       203       213 
                                                                              52A                            82A||               100-TYS|100I||||                                                                                                                  
                                                                                                              82B|               100A|||||100J|||                                                                                                                  
                                                                                                               82C                100B|||||100K||                                                                                                                  
                                                                                                                                   100C-TYS|100L|                                                                                                                  
                                                                                                                                    100D|||| 100M                                                                                                                  
                                                                                                                                     100E|||                                                                                                                       
                                                                                                                                      100F||                                                                                                                       
                                                                                                                                       100G|                                                                                                                       
                                                                                                                                        100H

Chain E from PDB  Type:PROTEIN  Length:312
 aligned with ENV_HV1Y2 | P35961 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:391
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478 
           ENV_HV1Y2     89 TENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTTSSSWETMEKGEIKNCSFNITTSIRDKVQKEYALFYNLDVVPIDNASYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  479
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) GP120-2qadE01 E:90-492                                                                                                                                                                                                                                                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) GP120-2qadE02 E:90-492                                                                                                                                                                                                                                                                                                                                                                                  Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhhhhhhh......eee...----------------------------------------------------------------------.eee............eee.....eeeeee.............eeee.............eee.........eeee.........eeeeeeeeeeeeeee....ee..eee..........ee.....eeeeeehhhhhhhhhhhhhhhhhhhhh....eee......hhhhhheeeee..eeeee..........---------.eeeeee...eee......eee........eeeeeeeeeeeeee.........eeeee...hhhhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qad E   90 TENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGG----------------------------------------------------------------------SVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWND---------NITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    99       109       119     |   -         -         -         -         -         -         -      |202       212       222       232       242       252       262       272       282       292       302      |314       323       333       343       353       363       373       383       393 |       - |     421       431       441       451       461       471       481       491 
                                                             125                                                                    199                                                                                                           309|       322A                                                                      395       413                                                                               
                                                                                                                                                                                                                                                   312

Chain F from PDB  Type:PROTEIN  Length:179
 aligned with CD4_HUMAN | P01730 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:179
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195         
           CD4_HUMAN     26 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAF  204
               SCOP domains d2qadf1 F:1-97 CD4 V-set domains                                                                 d2qadf2 F:98-178 CD4 C2-set domains                                              - SCOP domains
               CATH domains 2qadF01 F:1-98 Immunoglobulins                                                                    2qadF02 F:99-173 Immunoglobulins                                           ------ CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------C2-set-2qadF01 F:100-178                                                       - Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------C2-set-2qadF02 F:100-178                                                       - Pfam domains (2)
           Pfam domains (3) V-set-2qadF03 F:1-105                                                                                    -------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) V-set-2qadF04 F:1-105                                                                                    -------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeee....eee............eee.....eeee...................hhhhhhhh...eee.........eee........eeeeeeeeeee....ee.....eeeeee.........ee.......ee...eeee...hhhhheee..eee....eee..eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------E------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: F:1-47 UniProt: 17-72           ----------------------------------------------------Exon 1.5  PDB: F:100-178 UniProt: 125-203                                      - Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.4  PDB: F:47-100 UniProt: 72-125               -----------------------------------------------------------------------------1. Transcript 1 (2)
                2qad F    1 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAF  179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain G from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qadG01 G:1-108 Immunoglobulins                                                                             -2qadG02 G:110-211 Immunoglobulins                                                                     -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeee.....eeeeee.........eeeee......eeeee...ee.......eeeeee..eeeeee.........eeeee............eeeee........eeee..hhhhhh..ee..eeeeeee.................................eee.....eehhhhhh......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qad G    1 DIQMTQSPSTLSASVGDRVTITCRASQSISNWLAWYQQKPGRAPKLLMYKASSLKSGVPSRFSGSGSGTEFTLTISSLQSDDFATYYCQQHDSSPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKLYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain H from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                        
               SCOP domains d2qadh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                    d2qadh2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 2qadH01 H:1-109 Immunoglobulins                                                                                               2qadH02 H:110-214 Immunoglobulins                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.....eee.eee...hhhhh..eeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeee...........................eeee..........................eee...........eee.........ee...ee.....ee..eee.............eee.hhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qad H    1 EVQLVQSGAEVKKPGSSVKVSCKASGGTFSNYAINWVRQAPGQGLEWMGGIIPIFNIAHYAQRFQGRVSITADESTSTAYMELSSLRSEDTAVFYCASPYPNDyNDyAPEEGMSWYFDLWGRGTLVTVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96   |||100F|||||||103       113       123       133       143       153       163       173       183       193       203       213 
                                                                              52A                            82A||               100-TYS|100I||||                                                                                                                  
                                                                                                              82B|               100A|||||100J|||                                                                                                                  
                                                                                                               82C                100B|||||100K||                                                                                                                  
                                                                                                                                   100C-TYS|100L|                                                                                                                  
                                                                                                                                    100D|||| 100M                                                                                                                  
                                                                                                                                     100E|||                                                                                                                       
                                                                                                                                      100F||                                                                                                                       
                                                                                                                                       100G|                                                                                                                       
                                                                                                                                        100H

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: yu2. (2)

1a	2qadC02	C:110-211
1b	2qadD02	D:110-214
1c	2qadH02	H:110-214
1d	2qadD01	D:1-109
1e	2qadH01	H:1-109
1f	2qadB01	B:1-98
1g	2qadF01	F:1-98
1h	2qadB02	B:99-173
1i	2qadF02	F:99-173
1j	2qadG02	G:110-211
1k	2qadC01	C:1-108
1l	2qadG01	G:1-108

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C2-set (18)

Homo sapiens (Human) (18)

1a	C2-set-2qadF01	F:100-178
1b	C2-set-2qadF02	F:100-178

Family: V-set (144)

Homo sapiens (Human) (61)

2a	V-set-2qadF03	F:1-105
2b	V-set-2qadF04	F:1-105

Clan: no clan defined [family: GP120] (26)

Family: GP120 (26)

Human immunodeficiency virus type 1 group M subtype B (isolate YU-2) (HIV-1) (3)

3a	GP120-2qadE01	E:90-492
3b	GP120-2qadE02	E:90-492

Asymmetric Unit(hide GO term definitions)

Chain A,E (ENV_HV1Y2 | P35961)

molecular function
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019082	viral protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Chain B,F (CD4_HUMAN | P01730)

molecular function
	GO:0042289	MHC class II protein binding	Interacting selectively and non-covalently with major histocompatibility complex class II molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
	GO:0015026	coreceptor activity	Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0005201	extracellular matrix structural constituent	The action of a molecule that contributes to the structural integrity of the extracellular matrix.
	GO:0019865	immunoglobulin binding	Interacting selectively and non-covalently with an immunoglobulin.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:1990782	protein tyrosine kinase binding	Interacting selectively and non-covalently with protein tyrosine kinase.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0042110	T cell activation	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0045058	T cell selection	The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0001816	cytokine production	The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0050829	defense response to Gram-negative bacterium	Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
	GO:0030260	entry into host cell	The invasion by an organism of a cell of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0007167	enzyme linked receptor protein signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0035397	helper T cell enhancement of adaptive immune response	Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0006948	induction by virus of host cell-cell fusion	The process of syncytia-forming cell-cell fusion, caused by a virus.
	GO:0032507	maintenance of protein location in cell	Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.
	GO:0050870	positive regulation of T cell activation	Any process that activates or increases the frequency, rate or extent of T cell activation.
	GO:0042102	positive regulation of T cell proliferation	Any process that activates or increases the rate or extent of T cell proliferation.
	GO:0010524	positive regulation of calcium ion transport into cytosol	Any process that increases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components.
	GO:0050850	positive regulation of calcium-mediated signaling	Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling.
	GO:0045086	positive regulation of interleukin-2 biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2.
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0045860	positive regulation of protein kinase activity	Any process that activates or increases the frequency, rate or extent of protein kinase activity.
	GO:0050863	regulation of T cell activation	Any process that modulates the frequency, rate or extent of T cell activation.
	GO:0050690	regulation of defense response to virus by virus	Any viral process that modulates the frequency, rate, or extent of the antiviral response of the host cell or organism.
	GO:0032355	response to estradiol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0033280	response to vitamin D	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin D stimulus.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0042101	T cell receptor complex	A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MLA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TYS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]
		CC9	[ RasMol ]	+environment [ RasMol ]
		DC1	[ RasMol ]	+environment [ RasMol ]
		DC2	[ RasMol ]	+environment [ RasMol ]
		DC3	[ RasMol ]	+environment [ RasMol ]
		DC4	[ RasMol ]	+environment [ RasMol ]
		DC5	[ RasMol ]	+environment [ RasMol ]
		DC6	[ RasMol ]	+environment [ RasMol ]
		DC7	[ RasMol ]	+environment [ RasMol ]
		DC8	[ RasMol ]	+environment [ RasMol ]
		DC9	[ RasMol ]	+environment [ RasMol ]
		EC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu D:148 - Pro D:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe D:146 - Pro D:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]
		Ser C:94 - Pro C:95	[ RasMol ]
		Ser G:7 - Pro G:8	[ RasMol ]
		Ser G:94 - Pro G:95	[ RasMol ]
		Tyr C:140 - Pro C:141	[ RasMol ]
		Tyr G:140 - Pro G:141	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2qad
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	A4F255_HUMAN \| A4F255
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	CD4_HUMAN \| P01730
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	ENV_HV1Y2 \| P35961
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	IGHG1_HUMAN \| P01857
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	A4F255_HUMAN \| A4F255
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	CD4_HUMAN \| P01730
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	ENV_HV1Y2 \| P35961
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	IGHG1_HUMAN \| P01857
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 2QAD)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 46)

Sites (37, 37)

SS Bonds (24, 24)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (0, 0)

Exons (4, 8)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 8)

CATH Domains (1, 12)

Pfam Domains (3, 6)

Gene Ontology (90, 96)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File