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2B4C
Asym. Unit
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 not available)
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, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
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Exons
(3, 3)
Info
All Exons
Exon 1.3 (C:1-47)
Exon 1.4 (C:47-100)
Exon 1.5 (C:100-175)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3
2: Boundary 1.3/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6b
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000011653
1
ENSE00001303311
chr12:
6898651-6898828
178
CD4_HUMAN
-
0
0
-
-
1.2
ENST00000011653
2
ENSE00000866954
chr12:
6909238-6909353
116
CD4_HUMAN
1-17
17
0
-
-
1.3
ENST00000011653
3
ENSE00000716042
chr12:
6909473-6909637
165
CD4_HUMAN
17-72
56
1
C:1-47
47
1.4
ENST00000011653
4
ENSE00000716044
chr12:
6923308-6923466
159
CD4_HUMAN
72-125
54
1
C:47-100
54
1.5
ENST00000011653
5
ENSE00000716046
chr12:
6923925-6924158
234
CD4_HUMAN
125-203
79
1
C:100-175
76
1.6b
ENST00000011653
6b
ENSE00000716048
chr12:
6925222-6925569
348
CD4_HUMAN
203-319
117
0
-
-
1.7
ENST00000011653
7
ENSE00000716051
chr12:
6926296-6926496
201
CD4_HUMAN
319-386
68
0
-
-
1.8
ENST00000011653
8
ENSE00000716053
chr12:
6927587-6927708
122
CD4_HUMAN
386-426
41
0
-
-
1.9
ENST00000011653
9
ENSE00000716057
chr12:
6928013-6928080
68
CD4_HUMAN
427-449
23
0
-
-
1.10
ENST00000011653
10
ENSE00001182623
chr12:
6928465-6929976
1512
CD4_HUMAN
449-458
10
0
-
-
[
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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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Classes
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)
(
)
Folds
(
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(
)
Superfamilies
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)
(
)
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
View:
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Sorry, no Info available
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Sidechain
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Solvent
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain C
Chain G
Chain H
Chain L
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Asym.Unit (162 KB)
Header - Asym.Unit
Biol.Unit 1 (156 KB)
Header - Biol.Unit 1
Biol.Unit 2 (608 KB)
Header - Biol.Unit 2
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