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3IDX
Asym. Unit
Info
Asym.Unit (272 KB)
Biol.Unit 1 (263 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIV-GP120 CORE IN COMPLEX WITH CD4-BINDING SITE ANTIBODY B13, SPACE GROUP C222
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
:
2.50
Chains
:
Asym. Unit : G,H,L
Biol. Unit 1: 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
(4, 23)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
2a: GLYCEROL (GOLa)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
2
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
GOL
1
Ligand/Ion
GLYCEROL
3
NAG
16
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN G:88 , HOH G:1040
BINDING SITE FOR RESIDUE NAG G 588
02
AC2
SOFTWARE
SER G:195 , ASN G:197 , HOH G:1148
BINDING SITE FOR RESIDUE NAG G 697
03
AC3
SOFTWARE
ASN G:230 , THR G:232 , ASN G:234 , THR G:240 , NAG G:734
BINDING SITE FOR RESIDUE NAG G 730
04
AC4
SOFTWARE
ASN G:234 , THR G:236 , PRO G:238 , NAG G:730
BINDING SITE FOR RESIDUE NAG G 734
05
AC5
SOFTWARE
ASN G:229 , ASN G:241 , ASP G:412
BINDING SITE FOR RESIDUE NAG G 741
06
AC6
SOFTWARE
GLU G:211 , ASN G:262 , ASN G:377 , ILE G:443 , ARG G:444 , SER G:446 , SER G:447 , NAG G:948 , HOH G:1119 , HOH G:1142
BINDING SITE FOR RESIDUE NAG G 762
07
AC7
SOFTWARE
ASN G:276 , THR G:278 , ASP G:279
BINDING SITE FOR RESIDUE NAG G 776
08
AC8
SOFTWARE
GLU G:268 , GLU G:269 , VAL G:270 , ASN G:289 , THR G:290 , LYS G:337 , SO4 G:1002
BINDING SITE FOR RESIDUE NAG G 789
09
AC9
SOFTWARE
GLU G:267 , ASN G:295 , ASN G:332 , ALA G:334
BINDING SITE FOR RESIDUE NAG G 795
10
BC1
SOFTWARE
ARG G:335 , ASN G:339 , LYS G:343 , TRP G:395 , HOH G:1083 , HOH G:1088
BINDING SITE FOR RESIDUE NAG G 839
11
BC2
SOFTWARE
ASN G:356 , GLU G:464 , NAG G:897 , HOH G:1204
BINDING SITE FOR RESIDUE NAG G 856
12
BC3
SOFTWARE
ASN G:386 , THR G:388 , NAG G:892 , SO4 G:1004 , HOH G:1194 , HOH G:1224 , GLY H:100 , HOH H:1118
BINDING SITE FOR RESIDUE NAG G 886
13
BC4
SOFTWARE
GLN G:389 , ASN G:392 , NAG G:886
BINDING SITE FOR RESIDUE NAG G 892
14
BC5
SOFTWARE
THR G:358 , ASN G:397 , NAG G:856
BINDING SITE FOR RESIDUE NAG G 897
15
BC6
SOFTWARE
GLU G:293 , ARG G:444 , SER G:446 , ASN G:448 , NAG G:762 , GOL G:1006
BINDING SITE FOR RESIDUE NAG G 948
16
BC7
SOFTWARE
ASN G:463
BINDING SITE FOR RESIDUE NAG G 963
17
BC8
SOFTWARE
GLU G:370 , TYR G:384 , GLN G:422 , ILE G:423 , ILE G:424 , HOH G:1039 , HOH G:1220 , LYS H:52 , LEU H:100F , THR H:100G
BINDING SITE FOR RESIDUE EPE G 1000
18
BC9
SOFTWARE
GLN G:344 , NAG G:789 , HOH G:1037 , HOH G:1070
BINDING SITE FOR RESIDUE SO4 G 1002
19
CC1
SOFTWARE
PRO G:253 , VAL G:254 , ASN G:478 , TRP G:479 , GLU G:482 , HOH G:1182
BINDING SITE FOR RESIDUE SO4 G 1003
20
CC2
SOFTWARE
ASN G:386 , ARG G:419 , NAG G:886 , HOH G:1224 , ILE H:100E
BINDING SITE FOR RESIDUE SO4 G 1004
21
CC3
SOFTWARE
LYS G:362 , ARG G:469
BINDING SITE FOR RESIDUE SO4 G 1005
22
CC4
SOFTWARE
ASN G:262 , GLY G:263 , SER G:291 , NAG G:948
BINDING SITE FOR RESIDUE GOL G 1006
23
CC5
SOFTWARE
LYS G:282 , ARG G:476 , ARG H:30 , ARG H:71 , ASP H:72 , ASN H:73 , SER H:74 , HOH H:1135
BINDING SITE FOR RESIDUE EPE H 1001
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3idxl1 (L:1-107)
2a: SCOP_d3idxl2 (L:108-213)
3a: SCOP_d3idxg_ (G:)
View:
Select:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Human (Homo sapiens) [TaxId: 9606]
(448)
1a
d3idxl1
L:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
2a
d3idxl2
L:108-213
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
gp120 core
(24)
Superfamily
:
gp120 core
(24)
Family
:
gp120 core
(24)
Protein domain
:
gp120 core
(19)
Human immunodeficiency virus type 1 [TaxId: 11676]
(18)
3a
d3idxg_
G:
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_3idxL02 (L:108-211)
1b: CATH_3idxH02 (H:114-216)
1c: CATH_3idxH01 (H:1-113)
View:
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(
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Topologies
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)
(
)
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
3idxL02
L:108-211
1b
3idxH02
H:114-216
1c
3idxH01
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
(currently selected atoms:
all
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Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain G
Chain H
Chain L
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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