1YYM - JenaLib

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)

Title :   CRYSTAL STRUCTURE OF F23, A SCORPION-TOXIN MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B

Authors :   C. C. Huang, F. Stricher, L. Martin, J. M. Decker, S. Majeed, P. Barthe, W. A. Hendrickson, J. Robinson, C. Roumestand, J. Sodroski, R. Wyatt, C. Vita, P. D. Kwong

Date :   25 Feb 05 (Deposition) - 03 May 05 (Release) - 14 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : G,H,L,M,P,Q,R,S
Biol. Unit 1: G,H,L,M  (1x)
Biol. Unit 2: P,Q,R,S  (1x)

Keywords :   Hiv-1, Gp120, Yu2, Scorpion Toxin, Cd4 Mimic, F23, Antibody, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. C. Huang, F. Stricher, L. Martin, J. M. Decker, S. Majeed, P. Barthe, W. A. Hendrickson, J. Robinson, C. Roumestand, J. Sodroski, R. Wyatt, G. M. Shaw, C. Vita, P. D. Kwong
Scorpion-Toxin Mimics Of Cd4 In Complex With Human Immunodeficiency Virus Gp120 Crystal Structures, Molecular Mimicry, And Neutralization Breadth.
Structure V. 13 755 2005
PubMed-ID: 15893666 | Reference-DOI: 10.1016/J.STR.2005.03.006

Molecule 1 - EXTERIOR MEMBRANE GLYCOPROTEIN(GP120),EXTERIOR MEMBRANE GLYCOPROTEIN(GP120),EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)
	Chains	:	G, P
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Taxid	:	7227
	Fragment	:	UNP RESIDUES 82-126,UNP RESIDUES 191-293,UNP RESIDUES 325- 479
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Synonym	:	HIV-1 YU2 GP120, ENVELOPE GLYCOPROTEIN GP160,HIV-1 YU2 GP120, ENVELOPE GLYCOPROTEIN GP160,HIV-1 YU2 GP120, ENVELOPE GLYCOPROTEIN GP160

Molecule 2 - ANTIBODY 17B LIGHT CHAIN
	Chains	:	L, Q
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	MOUSE
	Expression System Taxid	:	10090
	Fragment	:	ANTIGEN-BINDING FRAGMENT, FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	EPSTEIN-BARR VIRUS IMMORTALIZED B-CELLCLONE FUSED WITH A MURINE B-CELL FUSION PARTNER

Molecule 3 - ANTIBODY 17B HEAVY CHAIN
	Chains	:	H, R
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	MOUSE
	Expression System Taxid	:	10090
	Fragment	:	ANTIGEN-BINDING FRAGMENT, FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	EPSTEIN-BARR VIRUS IMMORTALIZED B-CELLCLONE FUSED WITH A MURINE B-CELL FUSION PARTNER

Molecule 4 - F23, SCORPION-TOXIN MIMIC OF CD4
	Chains	:	M, S
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	SYNTHETIC MINIPROTEIN (SOLID PHASE METHOD USING FMOC- PROTECTED AMINO ACIDS)
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	G	H	L	M	P	Q	R	S
Biological Unit 1 (1x)	:	G	H	L	M
Biological Unit 2 (1x)	:					P	Q	R	S

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 24)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
3	MPT	2	Mod. Amino Acid	BETA-MERCAPTOPROPIONIC ACID
4	NAG	15	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	VLM	2	Mod. Amino Acid	VALINYLAMINE

Biological Unit 1 (6, 13)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
3	MPT	1	Mod. Amino Acid	BETA-MERCAPTOPROPIONIC ACID
4	NAG	7	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	VLM	1	Mod. Amino Acid	VALINYLAMINE

Biological Unit 2 (4, 11)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
3	MPT	1	Mod. Amino Acid	BETA-MERCAPTOPROPIONIC ACID
4	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	-1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	VLM	1	Mod. Amino Acid	VALINYLAMINE

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN G:88 , ASN G:241 , NAG G:741 , HOH G:999 , HOH G:1004 , HOH G:1029	BINDING SITE FOR RESIDUE NAG G 588
02	AC2	SOFTWARE	ASN G:234 , THR G:236	BINDING SITE FOR RESIDUE NDG G 734
03	AC3	SOFTWARE	THR G:240 , ASN G:241 , NAG G:588 , HOH G:914	BINDING SITE FOR RESIDUE NAG G 741
04	AC4	SOFTWARE	ARG G:252 , VAL G:254 , ASN G:262 , ASN G:377 , CYS G:378 , SER G:446 , SER G:447 , HOH G:1006	BINDING SITE FOR RESIDUE NAG G 762
05	AC5	SOFTWARE	ASN G:276 , THR G:278 , ASN G:279 , HOH G:1001	BINDING SITE FOR RESIDUE NAG G 776
06	AC6	SOFTWARE	GLU G:269 , ILE G:270 , ASN G:289 , GLU G:290 , GLN G:344 , LYS G:348 , HOH G:927 , HOH G:946 , LYS L:188	BINDING SITE FOR RESIDUE NAG G 789
07	AC7	SOFTWARE	GLU G:87 , ASN G:295 , SER G:446 , HOH G:983	BINDING SITE FOR RESIDUE NAG G 795
08	AC8	SOFTWARE	ASN G:386 , THR G:388 , GLN G:389 , HOH G:954 , GLY S:1014 , LEU S:1015 , LEU S:1016 , VLM S:1027	BINDING SITE FOR RESIDUE NAG G 886
09	AC9	SOFTWARE	HOH P:253 , ASN P:1088 , THR P:1240 , ASN P:1241 , NAG P:1741	BINDING SITE FOR RESIDUE NAG P 1588
10	BC1	SOFTWARE	ASN P:1234 , THR P:1236	BINDING SITE FOR RESIDUE NAG P 1734
11	BC2	SOFTWARE	HOH P:208 , ASP P:1230 , LYS P:1231 , ASN P:1241 , NAG P:1588 , LYS Q:1188	BINDING SITE FOR RESIDUE NAG P 1741
12	BC3	SOFTWARE	HOH P:550 , HOH P:571 , HOH P:785 , VAL P:1254 , ASN P:1262 , ASN P:1377 , CYS P:1378 , SER P:1446 , SER P:1447	BINDING SITE FOR RESIDUE NAG P 1762
13	BC4	SOFTWARE	LYS G:460 , HOH P:236 , ASN P:1276 , THR P:1278 , ASN P:1279	BINDING SITE FOR RESIDUE NAG P 1776
14	BC5	SOFTWARE	HOH P:243 , GLU P:1268 , GLU P:1269 , ILE P:1270 , ASN P:1289 , GLN P:1344 , GLY Q:1212	BINDING SITE FOR RESIDUE NAG P 1789
15	BC6	SOFTWARE	HOH P:656 , GLU P:1087 , ASN P:1295 , SER P:1446	BINDING SITE FOR RESIDUE NAG P 1795
16	BC7	SOFTWARE	HOH P:274 , ASN P:1386 , THR P:1388 , GLN P:1389	BINDING SITE FOR RESIDUE NAG P 1886
17	BC8	SOFTWARE	PRO G:253 , VAL G:254 , LEU G:261 , ASN G:478 , TRP G:479 , HOH G:911	BINDING SITE FOR RESIDUE EDO G 903
18	BC9	SOFTWARE	SER M:12	BINDING SITE FOR RESIDUE EDO M 904
19	CC1	SOFTWARE	SER G:375 , PHE G:376 , TYR G:384 , PHE M:23	BINDING SITE FOR RESIDUE IPA G 901
20	CC2	SOFTWARE	HOH P:64 , VAL P:1255 , SER P:1375 , PHE P:1376 , ASN P:1377	BINDING SITE FOR RESIDUE IPA P 902

Asymmetric Unit

No.	Residues
1	G:119	-	G:205
2	G:126	-	G:196
3	G:218	-	G:247
4	G:228	-	G:239
5	G:296	-	G:331
6	G:331	-	G:418
7	G:378	-	G:445
8	G:385	-	G:418
9	H:22	-	H:92
10	H:140	-	H:196
11	L:23	-	L:88
12	L:134	-	L:194
13	M:6	-	M:24
14	M:10	-	M:26
15	P:1119	-	P:1205
16	P:1126	-	P:1196
17	P:1218	-	P:1247
18	P:1228	-	P:1239
19	P:1296	-	P:1331
20	P:1378	-	P:1445
21	P:1385	-	P:1418
22	Q:1023	-	Q:1088
23	Q:1134	-	Q:1194
24	R:1022	-	R:1092
25	R:1140	-	R:1196
26	S:1006	-	S:1024
27	S:1010	-	S:1026

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Trp L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Ser Q:1007	-	Pro Q:1008
7	Trp Q:1094	-	Pro Q:1095
8	Tyr Q:1140	-	Pro Q:1141
9	Phe R:1146	-	Pro R:1147
10	Glu R:1148	-	Pro R:1149

(no "SAP(SNP)/Variant" information available for 1YYM)

(no "PROSITE Motif" information available for 1YYM)

(no "Exon" information available for 1YYM)

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 G from PDB  Type:PROTEIN  Length:301
 aligned with ENV_HV1Y2 | P35961 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:398
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
          ENV_HV1Y2      82 EVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTTSSSWETMEKGEIKNCSFNITTSIRDKVQKEYALFYNLDVVPIDNASYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE   479
               SCOP domains d1yymg_ G: automated matches                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1yymG00 G:83-492 HIV Envelope Protein Gp120; Ch                                                             ain G                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee...hhhhhhhhhhhhhhhhhhh...eeeeeee...-------------------------------------------------------------..eeeeeee....................eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeee..----------------------------.eeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee..hhhhhee.--------.eeeeeeee..eee......eee.........eeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
               1yym G    83 EVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGA-------------------------------------------------------------GSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGA----------------------------GHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWND--------RNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE   492
                                    92       102       112       122      |  -         -         -         -         -         -       195       205       215       225       235       245       255       265       275       285       295   |     -         -         -  |    336       346       356       366       376       386        |-       414       424       434       444       454       464       474       484        
                                                                        129                                                           194                                                                                                      299                          329                                                               395      412

Chain H from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                       
               SCOP domains d1yymh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                  d1yymh2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1yymH01 H:1-113 Immunoglobulins                                                                                                 1yymH02 H:114-213 Immunoglobulins                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..hhhhh.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
               1yym H     1 EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK   214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105       115       125       135       145       155       165       175       185       195       205         
                                                                              52A                            82A||               100A|||||100J|                                                                                                                  
                                                                                                              82B|                100B|||||100K                                                                                                                  
                                                                                                               82C                 100C||||||                                                                                                                    
                                                                                                                                    100D|||||                                                                                                                    
                                                                                                                                     100E||||                                                                                                                    
                                                                                                                                      100F|||                                                                                                                    
                                                                                                                                       100G||                                                                                                                    
                                                                                                                                        100H|                                                                                                                    
                                                                                                                                         100I

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                        
               SCOP domains d1yyml1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                   d1yyml2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1yymL01 L:1-108 Immunoglobulins                                                                               1yymL02 L:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee........ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
               1yym L     1 DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG   212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B

Chain M from PDB  Type:PROTEIN  Length:27
                                                             
               SCOP domains -d1yymm1 M:2-27             SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
               1yym M     1 xNLHFCQLRCKSLGLLGKCAGSFCACx    27
                            |       10        20      |
                            1-MPT                    27-VLM

Chain P from PDB  Type:PROTEIN  Length:299
 aligned with ENV_HV1Y2 | P35961 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:398
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
          ENV_HV1Y2      82 EVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTTSSSWETMEKGEIKNCSFNITTSIRDKVQKEYALFYNLDVVPIDNASYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE   479
               SCOP domains d1yymp_ P: automated matches                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1yymP00 P:1083-1492 HIV Envelope Protein Gp120;                                                              Chain G                                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) GP120-1yymP01 P:1083-1492                                                                                                                                                                                                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) GP120-1yymP02 P:1083-1492                                                                                                                                                                                                                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ........eeee...hhhhhhhhhhhhhhhhhhh...eeeeeee...-------------------------------------------------------------..eeeeeee....................eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeee...----------------------------.eeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh..----------.eeeeeeee..eee......eee..........eeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
               1yym P  1083 EVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGA-------------------------------------------------------------GSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGA----------------------------GHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTW----------RNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  1492
                                  1092      1102      1112      1122      |  -         -         -         -         -         -      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295   |     -         -         -  |   1336      1346      1356      1366      1376      1386      |  -      1414      1424      1434      1444      1454      1464      1474      1484        
                                                                       1129                                                          1194                                                                                                     1299                         1329                                                            1393       1412

Chain Q from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                        
               SCOP domains d1yymq1 Q:1001-1107 Immunoglobulin light chain kappa variable domain, VL-kappa                               d1yymq2 Q:1108-1212 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains 1yymQ01 Q:1001-1108 Immunoglobulins                                                                           1yymQ02 Q:1109-1211 Immunoglobulins                                                                    - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee........ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
               1yym Q  1001 DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  1212
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090     |1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208    
                                                                                                                       1095A|                                                                                                                     
                                                                                                                        1095B

Chain R from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                       
               SCOP domains d1yymr1 R:1001-1113 Immunoglobulin heavy chain variable domain, VH                                                              d1yymr2 R:1114-1214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1yymR01 R:1001-1113 Immunoglobulins                                                                                             1yymR02 R:1114-1213 Immunoglobulins                                                                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee..hhhhh.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
               1yym R  1001 EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  1214
                                  1010      1020      1030      1040      1050  |   1059      1069      1079   |||1086      1096    |1100F||||| 1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205         
                                                                            1052A                          1082A||              1100A||||1100J|                                                                                                                  
                                                                                                            1082B|               1100B||||1100K                                                                                                                  
                                                                                                             1082C                1100C||||||                                                                                                                    
                                                                                                                                   1100D|||||                                                                                                                    
                                                                                                                                    1100E||||                                                                                                                    
                                                                                                                                     1100F|||                                                                                                                    
                                                                                                                                      1100G||                                                                                                                    
                                                                                                                                       1100H|                                                                                                                    
                                                                                                                                        1100I

Chain S from PDB  Type:PROTEIN  Length:27
                                                             
               SCOP domains -d1yyms1 S:1002-1027        SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
               1yym S  1001 xNLHFCQLRCKSLGLLGKCAGSFCACx  1027
                            |     1010      1020      |
                         1001-MPT                  1027-VLM

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: Beta Complex (381)

Topology: HIV Envelope Protein Gp120; Chain G (17)

Homologous Superfamily: HIV Envelope Protein Gp120; Chain G (17)

Human immunodeficiency virus 1. Organism_taxid: 11676. (3)

1a	1yymG00	G:83-492
1b	1yymP00	P:1083-1492

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human immunodeficiency virus 1. Organism_taxid: 11676. (3)

2a	1yymL02	L:109-211
2b	1yymQ02	Q:1109-1211
2c	1yymH02	H:114-213
2d	1yymR02	R:1114-1213
2e	1yymH01	H:1-113
2f	1yymR01	R:1001-1113
2g	1yymL01	L:1-108
2h	1yymQ01	Q:1001-1108

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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)

1a	GP120-1yymP01	P:1083-1492
1b	GP120-1yymP02	P:1083-1492

Asymmetric Unit(hide GO term definitions)

Chain G,P (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.

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1yyl	CD4M33 COMPLEXED WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 24)

Sites (20, 20)

SS Bonds (27, 27)

Cis Peptide Bonds (10, 10)

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SAPs(SNPs)/Variants (0, 0)

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SCOP Domains (6, 12)

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