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2B4C
Biol. Unit 1
Info
Asym.Unit (162 KB)
Biol.Unit 1 (156 KB)
Biol.Unit 2 (608 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIV-1 JR-FL GP120 CORE PROTEIN CONTAINING THE THIRD VARIABLE REGION (V3) COMPLEXED WITH CD4 AND THE X5 ANTIBODY
Authors
:
C. Huang, M. Tang, M. Y. Zhang, S. Majeed, E. Montabana, R. L. Stanfield, D. S. Dimitrov, B. Korber, J. Sodroski, I. A. Wilson, R. Wyatt, P. D. Kwo
Date
:
23 Sep 05 (Deposition) - 15 Nov 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : C,G,H,L
Biol. Unit 1: C,G,H,L (1x)
Biol. Unit 2: C,G,H,L (4x)
Keywords
:
Hiv-1, Gp120, Jrfl, V3, X5, Cd4 Induced Antibody, Viral Protein- Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. C. Huang, M. Tang, M. Y. Zhang, S. Majeed, E. Montabana, R. L. Stanfield, D. S. Dimitrov, B. Korber, J. Sodroski, I. A. Wilson, R. Wyatt, P. D. Kwong
Structure Of A V3-Containing Hiv-1 Gp120 Core.
Science V. 310 1025 2005
[
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Hetero Components
(5, 13)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
3b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
5a: D-XYLITOL (XYLa)
5b: D-XYLITOL (XYLb)
5c: D-XYLITOL (XYLc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
2
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4
SO4
5
Ligand/Ion
SULFATE ION
5
XYL
3
Ligand/Ion
D-XYLITOL
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG G:252 , ASN G:262 , CYS G:378 , SER G:446 , SER G:447
BINDING SITE FOR RESIDUE NAG G 762
02
AC2
SOFTWARE
ASN G:276 , FUC G:777
BINDING SITE FOR RESIDUE NDG G 776
03
AC3
SOFTWARE
GLN C:33 , LYS C:90 , NDG G:776
BINDING SITE FOR RESIDUE FUC G 777
04
AC4
SOFTWARE
THR G:297 , ASN G:332 , THR G:413 , THR G:415
BINDING SITE FOR RESIDUE NDG G 832
05
AC5
SOFTWARE
ASN G:362 , HIS G:363 , ASN G:392 , ARG G:469
BINDING SITE FOR RESIDUE NAG G 862
06
AC6
SOFTWARE
SER H:7 , GLY H:8 , LYS H:201
BINDING SITE FOR RESIDUE XYL H 217
07
AC7
SOFTWARE
LYS H:23 , GLY H:27
BINDING SITE FOR RESIDUE XYL H 218
08
AC8
SOFTWARE
ASN H:199 , LYS H:206
BINDING SITE FOR RESIDUE XYL H 219
09
AC9
SOFTWARE
GLY H:27 , THR H:28 , TYR H:32 , ARG H:94
BINDING SITE FOR RESIDUE SO4 H 220
10
BC1
SOFTWARE
PRO L:8 , GLY L:9
BINDING SITE FOR RESIDUE SO4 L 215
11
BC2
SOFTWARE
LYS H:12 , VAL H:18 , GLN H:19
BINDING SITE FOR RESIDUE SO4 H 221
12
BC3
SOFTWARE
LYS H:206 , ASP H:208
BINDING SITE FOR RESIDUE SO4 H 222
13
BC4
SOFTWARE
ALA G:204 , CYS G:205 , ILE H:53
BINDING SITE FOR RESIDUE SO4 G 5
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_023459 (K166E, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_023459
K
191
E
CD4_HUMAN
Polymorphism
28917504
C
K
166
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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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
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(7, 7)
Info
All SCOP Domains
1a: SCOP_d2b4ch2 (H:114-212)
2a: SCOP_d2b4cl2 (L:108-214)
3a: SCOP_d2b4cc2 (C:98-175)
4a: SCOP_d2b4cc1 (C:1-97)
5a: SCOP_d2b4ch1 (H:4-113)
6a: SCOP_d2b4cl1 (L:1-107)
7a: SCOP_d2b4cg1 (G:84-492)
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(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Human (Homo sapiens) [TaxId: 9606]
(179)
1a
d2b4ch2
H:114-212
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d2b4cl2
L:108-214
Family
:
C2 set domains
(47)
Protein domain
:
CD4 C2-set domains
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
3a
d2b4cc2
C:98-175
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
CD4 V-set domains
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
4a
d2b4cc1
C:1-97
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Human (Homo sapiens), cluster 4 [TaxId: 9606]
(4)
5a
d2b4ch1
H:4-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
(31)
6a
d2b4cl1
L:1-107
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)
7a
d2b4cg1
G:84-492
[
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CATH Domains
(2, 7)
Info
all CATH domains
1a: CATH_2b4cG00 (G:84-492)
2a: CATH_2b4cL02 (L:109-211)
2b: CATH_2b4cH02 (H:114-213)
2c: CATH_2b4cH01 (H:2-113)
2d: CATH_2b4cC01 (C:1-98)
2e: CATH_2b4cC02 (C:99-173)
2f: CATH_2b4cL01 (L:1-108)
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Classes
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)
(
)
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)
(
)
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
2b4cG00
G:84-492
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human immunodeficiency virus 1. Organism_taxid: 11676.
(3)
2a
2b4cL02
L:109-211
2b
2b4cH02
H:114-213
2c
2b4cH01
H:2-113
2d
2b4cC01
C:1-98
2e
2b4cC02
C:99-173
2f
2b4cL01
L:1-108
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain C
Chain G
Chain H
Chain L
Asymmetric Unit 1
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Asym.Unit (162 KB)
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Header - Biol.Unit 1
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