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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 HIV-GP120 CORE IN COMPLEX WITH CD4-BINDING SITE ANTIBODY B13, SPACE GROUP C2221

Authors :   L. Chen, Y. D. Kwon, T. Zhou, X. Wu, S. O'Dell, L. Cavacini, A. J. Hessell, M. Pancera, M. Tang, L. Xu, Z. Y. Yang, M. Y. Zhang, J. Arthos, D. R. Burto D. S. Dimitrov, G. J. Nabel, M. Posner, J. Sodroski, R. Wyatt, J. R. Masc P. D. Kwong

Date :   22 Jul 09 (Deposition) - 17 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym. Unit : A,B,C,G,H,L
Biol. Unit 1: A,B,C,G,H,L  (1x)
Biol. Unit 2: A,B,C,G,H,L  (1x)

Keywords :   Hiv-1, Antibody, Gp120, B13, Envelope Glycan Protein, Cd4-Binding Site, Aids, Apoptosis, Cell Membrane, Cleavage On Pair Of Basic Residues, Disulfide Bond, Envelope Protein, Fusion Protein, Host- Virus Interaction, Membrane, Transmembrane, Viral Immunoevasion, Virion, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Chen, Y. Do Kwon, T. Zhou, X. Wu, S. O'Dell, L. Cavacini, A. J. Hessell, M. Pancera, M. Tang, L. Xu, Z. Y. Yang, M. Y. Zhang, J. Arthos, D. R. Burton, D. S. Dimitrov, G. J. Nabel, M. R. Posner, J. Sodroski, R. Wyatt, J. R. Mascola, P. D. Kwong
Structural Basis Of Immune Evasion At The Site Of Cd4 Attachment On Hiv-1 Gp120.
Science V. 326 1123 2009
PubMed-ID: 19965434 | Reference-DOI: 10.1126/SCIENCE.1175868

Molecule 1 - HIV-1 HXBC2 GP120 CORE
	Chains	:	G, A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Plasmid	:	PCDNA3.1(-)
	Expression System Strain	:	293F
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	ENV
	Mutation	:	YES
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Strain	:	HXBC2

Molecule 2 - FAB B13 HEAVY CHAIN
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Plasmid	:	PCDNA3.1(-)
	Expression System Strain	:	293F
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - FAB B13 LIGHT CHAIN
	Chains	:	L, C
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Plasmid	:	PCDNA3.1(-)
	Expression System Strain	:	293F
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	G	H	L
Biological Unit 1 (1x)	:	A	B	C	G	H	L
Biological Unit 2 (1x)	:	A	B	C	G	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 29)

No.	Name	Count	Type	Full Name
1	NAG	28	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 29)

No.	Name	Count	Type	Full Name
1	NAG	28	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 29)

No.	Name	Count	Type	Full Name
1	NAG	28	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (29, 29)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN G:88	BINDING SITE FOR RESIDUE NAG G 588
02	AC2	SOFTWARE	ASN G:230 , THR G:232 , ASN G:234 , THR G:240 , NAG G:734	BINDING SITE FOR RESIDUE NAG G 730
03	AC3	SOFTWARE	HOH G:78 , PHE G:233 , ASN G:234 , PRO G:238 , NAG G:730	BINDING SITE FOR RESIDUE NAG G 734
04	AC4	SOFTWARE	ASP A:412 , ASN G:229 , ASN G:241	BINDING SITE FOR RESIDUE NAG G 741
05	AC5	SOFTWARE	GLU G:211 , VAL G:254 , ASN G:262 , ASN G:377 , ARG G:444 , SER G:447 , NAG G:948	BINDING SITE FOR RESIDUE NAG G 762
06	AC6	SOFTWARE	ASN G:276 , THR G:278	BINDING SITE FOR RESIDUE NAG G 776
07	AC7	SOFTWARE	LYS A:337 , GLU G:269 , VAL G:270 , ASN G:289 , GLN G:344	BINDING SITE FOR RESIDUE NAG G 789
08	AC8	SOFTWARE	GLU G:293 , ASN G:295 , ALA G:334	BINDING SITE FOR RESIDUE NAG G 795
09	AC9	SOFTWARE	ARG G:335 , ASN G:339	BINDING SITE FOR RESIDUE NAG G 839
10	BC1	SOFTWARE	ASN G:356 , PHE G:396 , SER G:398 , GLU G:464	BINDING SITE FOR RESIDUE NAG G 856
11	BC2	SOFTWARE	VAL G:372 , ASN G:386 , THR G:388 , LEU H:98 , GLY H:100	BINDING SITE FOR RESIDUE NAG G 886
12	BC3	SOFTWARE	ASN G:392 , HOH G:506	BINDING SITE FOR RESIDUE NAG G 892
13	BC4	SOFTWARE	NAG A:948 , GLU G:293 , ARG G:444 , SER G:446 , SER G:447 , ASN G:448 , NAG G:762	BINDING SITE FOR RESIDUE NAG G 948
14	BC5	SOFTWARE	ASN G:460 , SER G:461 , ASN G:463 , GLU G:464	BINDING SITE FOR RESIDUE NAG G 963
15	BC6	SOFTWARE	HOH G:66 , HOH G:68 , LYS G:362 , ARG G:469	BINDING SITE FOR RESIDUE SO4 G 1003
16	BC7	SOFTWARE	ASN A:88	BINDING SITE FOR RESIDUE NAG A 588
17	BC8	SOFTWARE	ASN A:230 , THR A:232 , ASN A:234 , THR A:240 , NAG A:734	BINDING SITE FOR RESIDUE NAG A 730
18	BC9	SOFTWARE	HOH A:51 , ASN A:234 , THR A:236 , PHE A:277 , NAG A:730	BINDING SITE FOR RESIDUE NAG A 734
19	CC1	SOFTWARE	ASN A:229 , ASN A:241	BINDING SITE FOR RESIDUE NAG A 741
20	CC2	SOFTWARE	GLU A:211 , VAL A:254 , ASN A:262 , ASN A:377 , ARG A:444 , SER A:447 , NAG A:948	BINDING SITE FOR RESIDUE NAG A 762
21	CC3	SOFTWARE	ASN A:276	BINDING SITE FOR RESIDUE NAG A 776
22	CC4	SOFTWARE	GLU A:268 , GLU A:269 , VAL A:270 , ASN A:289 , LYS G:337	BINDING SITE FOR RESIDUE NAG A 789
23	CC5	SOFTWARE	GLU A:293 , ASN A:295 , ILE A:333 , ALA A:334 , GLU G:267	BINDING SITE FOR RESIDUE NAG A 795
24	CC6	SOFTWARE	ASN A:339	BINDING SITE FOR RESIDUE NAG A 839
25	CC7	SOFTWARE	ASN A:356 , THR A:358 , PHE A:396 , SER A:398 , GLY G:354	BINDING SITE FOR RESIDUE NAG A 856
26	CC8	SOFTWARE	ASN A:386 , THR A:388 , GLY B:100 , TYR B:100C	BINDING SITE FOR RESIDUE NAG A 886
27	CC9	SOFTWARE	ASN A:392	BINDING SITE FOR RESIDUE NAG A 892
28	DC1	SOFTWARE	GLU A:293 , ARG A:444 , SER A:446 , SER A:447 , ASN A:448 , NAG A:762 , NAG G:948	BINDING SITE FOR RESIDUE NAG A 948
29	DC2	SOFTWARE	ASN A:463	BINDING SITE FOR RESIDUE NAG A 963

Asymmetric Unit

No.	Residues
1	A:96	-	A:275
2	A:109	-	A:428
3	A:119	-	A:205
4	A:126	-	A:196
5	A:218	-	A:247
6	A:228	-	A:239
7	A:296	-	A:331
8	A:378	-	A:445
9	A:385	-	A:418
10	B:22	-	B:92
11	B:140	-	B:196
12	C:23	-	C:88
13	C:134	-	C:194
14	G:96	-	G:275
15	G:109	-	G:428
16	G:119	-	G:205
17	G:126	-	G:196
18	G:218	-	G:247
19	G:228	-	G:239
20	G:296	-	G:331
21	G:378	-	G:445
22	G:385	-	G:418
23	H:22	-	H:92
24	H:140	-	H:196
25	L:23	-	L:88
26	L:134	-	L:194

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3IDY)

(no "PROSITE Motif" information available for 3IDY)

(no "Exon" information available for 3IDY)

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:303
 aligned with ENV_HV1H2 | P04578 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:410
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492
           ENV_HV1H2     83 EVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE  492
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeehhhhhhhhhhhhhh....eeeee...eeeeee..-------------------------------------------------------------------...eeeeee....eeeee..........eeeeee........eee..eeee.............eee.........eeee.........eeeeeeeeeeeeee..-----------------------------.eeeeehhhhhhhhhhhhhhhhh......eeee......hhhhhheeeee..eeeee.......eee...-----------...eeeeeeeeee.hhhheee..eee...........eeeeeeeeeee.......eeeeee...hhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3idy A   83 EVVLVNVTENFNWCKNDMVEQMHEDICSLWDQSLKPCVKLTPLCV-------------------------------------------------------------------SCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSSQLLLNGSLAEEEVVIRSCNFTDNAKTIIVQLNTSVEINCTGA-----------------------------GHCNIARAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHWFNCGGEFFYCNSTQLFNSTWFNS-----------GSDTITLPCRIKQIINMWCKVGKMMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    92       102       112       122    |    -         -         -         -         -         -         -  |    202       212       222       232       242       252       262       272       282       292      |  -         -         -      |332       342       352       362       372       382       392     |   -       412       422       432       442       452       462       472       482       492
                                                                      127                                                                 195                                                                                                     299                           329                                                                  398         410

Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3idyB01 B:1-113 Immunoglobulins                                                                                                 3idyB02 B:114-216 Immunoglobulins                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..ee......eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee...............eeee....eee.........eeeee........eeeeeeeeeee.......ee.hhh.....ee..........eeeeeeeeee.hhh....eeee..hhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3idy B    1 QVQLVESGGGVVQPGRSLRLSCAASGFTFRNYAMHWVRQAPGKGLEWVALIKYDGRNKYYADSVKGRFSISRDNSKNTLYLEMNSLRAEDTAVYYCARDIGLKGEHYDILTAYGPDYWGQGALVTVSSASTKGPSVFPLAPSSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105       115       125  ||   137       147       157       167       177       187       197       207         
                                                                              52A                            82A||               100A|||||100J|                         128|                                                                                     
                                                                                                              82B|                100B|||||100K                          131                                                                                     
                                                                                                               82C                 100C||||||                                                                                                                    
                                                                                                                                    100D|||||                                                                                                                    
                                                                                                                                     100E||||                                                                                                                    
                                                                                                                                      100F|||                                                                                                                    
                                                                                                                                       100G||                                                                                                                    
                                                                                                                                        100H|                                                                                                                    
                                                                                                                                         100I

Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------3idyC02 C:108-211 Immunoglobulins                                                                       -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee............eeeeee......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee........eeeee.........eeeeeeeeeehhhhhhh..eeeeeee......ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3idy C    1 DIQMTQSPSSLSASVGDRVTITCQASQDIRNYLNWYQQKPGKAPKLLIYDASNSETGVPSRFSGSGSGRDFTFTISSLQPEDVATYYCQQHQNVPLTTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90     |  99       109       119       129       139       149       159       169       179       189       199       209    
                                                                                                                         95A

Chain G from PDB  Type:PROTEIN  Length:306
 aligned with ENV_HV1H2 | P04578 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:410
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492
           ENV_HV1H2     83 EVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE  492
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeehhhhhhhhhhhhhh....eeee...eeeeeee....----------------------------------------------------------------....eeeeeee....eeee..........eeeeee........eee..eeee.............eee.........eeee.........eeeeeeeeeeeeee..-----------------------------.eeeeehhhhhhhhhhhhhhhhh......eeee......hhhhhheeeee..eeeee.......eee...-----------...eeeeeeeeee.hhhheee..eee...........eeeeeeeeeee.......eeeeee...hhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3idy G   83 EVVLVNVTENFNWCKNDMVEQMHEDICSLWDQSLKPCVKLTPLCVGA----------------------------------------------------------------GSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSSQLLLNGSLAEEEVVIRSCNFTDNAKTIIVQLNTSVEINCTGA-----------------------------GHCNIARAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHWFNCGGEFFYCNSTQLFNSTWFNS-----------GSDTITLPCRIKQIINMWCKVGKMMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    92       102       112       122      |  -         -         -         -         -         -         - |     202       212       222       232       242       252       262       272       282       292      |  -         -         -      |332       342       352       362       372       382       392     |   -       412       422       432       442       452       462       472       482       492
                                                                        129                                                              194                                                                                                      299                           329                                                                  398         410

Chain H from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3idyH01 H:1-113 Immunoglobulins                                                                                                 3idyH02 H:114-216 Immunoglobulins                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..ee......eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee...............eeee...eeee.........eeeee........eeeeeeeeeee.......ee.hhh.....ee..........eeeeeeeeee.hhh....eeee..hhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3idy H    1 QVQLVESGGGVVQPGRSLRLSCAASGFTFRNYAMHWVRQAPGKGLEWVALIKYDGRNKYYADSVKGRFSISRDNSKNTLYLEMNSLRAEDTAVYYCARDIGLKGEHYDILTAYGPDYWGQGALVTVSSASTKGPSVFPLAPSSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105       115       125  ||   137       147       157       167       177       187       197       207         
                                                                              52A                            82A||               100A|||||100J|                         128|                                                                                     
                                                                                                              82B|                100B|||||100K                          131                                                                                     
                                                                                                               82C                 100C||||||                                                                                                                    
                                                                                                                                    100D|||||                                                                                                                    
                                                                                                                                     100E||||                                                                                                                    
                                                                                                                                      100F|||                                                                                                                    
                                                                                                                                       100G||                                                                                                                    
                                                                                                                                        100H|                                                                                                                    
                                                                                                                                         100I

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------3idyL02 L:108-211 Immunoglobulins                                                                       -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee............eeeeee......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee........eeeee.........eeeeeeeeeehhhhhhh..eeeeeee......ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3idy L    1 DIQMTQSPSSLSASVGDRVTITCQASQDIRNYLNWYQQKPGKAPKLLIYDASNSETGVPSRFSGSGSGRDFTFTISSLQPEDVATYYCQQHQNVPLTTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90     |  99       109       119       129       139       149       159       169       179       189       199       209    
                                                                                                                         95A

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 '\|'

(no "SCOP Domain" information available for 3IDY)

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: hxbc2. (13)

1a	3idyC02	C:108-211
1b	3idyL02	L:108-211
1c	3idyB02	B:114-216
1d	3idyH02	H:114-216
1e	3idyB01	B:1-113
1f	3idyH01	H:1-113

(no "Pfam Domain" information available for 3IDY)

Asymmetric Unit(hide GO term definitions)

Chain A,G (ENV_HV1H2 | P04578)

molecular function
	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: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:0090527	actin filament reorganization	A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of actin filaments.
	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: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: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:1903905	positive regulation of establishment of T cell polarity	Any process that activates or increases the frequency, rate or extent of establishment of T cell polarity.
	GO:1903908	positive regulation of plasma membrane raft polarization	Any process that activates or increases the frequency, rate or extent of plasma membrane raft polarization.
	GO:1903911	positive regulation of receptor clustering	Any process that activates or increases the frequency, rate or extent of receptor clustering.
	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:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	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:0019068	virion assembly	A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
	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:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	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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3idx	CRYSTAL STRUCTURE OF HIV-GP120 CORE IN COMPLEX WITH CD4- BINDING SITE ANTIBODY B13. IN SPACE GROUP C222

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 29)

Sites (29, 29)

SS Bonds (26, 26)

Cis Peptide Bonds (10, 10)

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Gene Ontology (32, 32)

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