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3IDY
Asym. Unit
Info
Asym.Unit (527 KB)
Biol.Unit 1 (518 KB)
Biol.Unit 2 (518 KB)
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(1)
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
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Hetero Components
(2, 29)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
1ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
1l: N-ACETYL-D-GLUCOSAMINE (NAGl)
1m: N-ACETYL-D-GLUCOSAMINE (NAGm)
1n: N-ACETYL-D-GLUCOSAMINE (NAGn)
1o: N-ACETYL-D-GLUCOSAMINE (NAGo)
1p: N-ACETYL-D-GLUCOSAMINE (NAGp)
1q: N-ACETYL-D-GLUCOSAMINE (NAGq)
1r: N-ACETYL-D-GLUCOSAMINE (NAGr)
1s: N-ACETYL-D-GLUCOSAMINE (NAGs)
1t: N-ACETYL-D-GLUCOSAMINE (NAGt)
1u: N-ACETYL-D-GLUCOSAMINE (NAGu)
1v: N-ACETYL-D-GLUCOSAMINE (NAGv)
1w: N-ACETYL-D-GLUCOSAMINE (NAGw)
1x: N-ACETYL-D-GLUCOSAMINE (NAGx)
1y: N-ACETYL-D-GLUCOSAMINE (NAGy)
1z: N-ACETYL-D-GLUCOSAMINE (NAGz)
2a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
28
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(29, 29)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
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
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3idyC02 (C:108-211)
1b: CATH_3idyL02 (L:108-211)
1c: CATH_3idyB02 (B:114-216)
1d: CATH_3idyH02 (H:114-216)
1e: CATH_3idyB01 (B:1-113)
1f: CATH_3idyH01 (H:1-113)
View:
Select:
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Classes
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Homologous Superfamilies
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(
)
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
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Atom Selection
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
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Chain G
Chain H
Chain L
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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