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2NY4
Asym. Unit
Info
Asym.Unit (321 KB)
Biol.Unit 1 (313 KB)
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(1)
Title
:
HIV-1 GP120 ENVELOPE GLYCOPROTEIN (K231C, T257S, E268C, S334A, S375W) COMPLEXED WITH CD4 AND ANTIBODY 17B
Authors
:
T. Zhou, L. Xu, B. Dey, A. J. Hessell, D. Van Ryk, S. H. Xiang, X. Yang, M. Y M. B. Zwick, J. Arthos, D. R. Burton, D. S. Dimitrov, J. Sodroski, R. Wya G. J. Nabel, P. D. Kwong
Date
:
20 Nov 06 (Deposition) - 06 Feb 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Hiv, Gp120, Antibody, Cd4, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Zhou, L. Xu, B. Dey, A. J. Hessell, D. Van Ryk, S. H. Xiang, X. Yang, M. Y. Zhang, M. B. Zwick, J. Arthos, D. R. Burton, D. S. Dimitrov, J. Sodroski, R. Wyatt, G. J. Nabel, P. D. Kwong
Structural Definition Of A Conserved Neutralization Epitope On Hiv-1 Gp120.
Nature V. 445 732 2007
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Hetero Components
(3, 15)
Info
All Hetero Components
1a: HEXANE-1,6-DIOL (HEZa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2l: N-ACETYL-D-GLUCOSAMINE (NAGl)
2m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3a: SUCROSE (SUCa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEZ
1
Ligand/Ion
HEXANE-1,6-DIOL
2
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SUC
1
Ligand/Ion
SUCROSE
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Sites
(0, 0)
Info
All Sites
View:
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Label:
Sorry, no Info available
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_023459 (K1166E, chain B, )
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
B
K
1166
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(4, 4)
Info
All Exons
Exon 1.3 (B:1001-1047)
Exon 1.4 (B:1047-1100)
Exon 1.5 (B:1100-1178)
Exon 1.6b (B:1178-1181)
View:
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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
5: Boundary 1.6b/1.7
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
B:1001-1047
47
1.4
ENST00000011653
4
ENSE00000716044
chr12:
6923308-6923466
159
CD4_HUMAN
72-125
54
1
B:1047-1100
54
1.5
ENST00000011653
5
ENSE00000716046
chr12:
6923925-6924158
234
CD4_HUMAN
125-203
79
1
B:1100-1178
79
1.6b
ENST00000011653
6b
ENSE00000716048
chr12:
6925222-6925569
348
CD4_HUMAN
203-319
117
1
B:1178-1181
4
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_d2ny4d2 (D:3129-3229)
2a: SCOP_d2ny4c2 (C:2112-2214)
3a: SCOP_d2ny4b2 (B:1098-1181)
4a: SCOP_d2ny4b1 (B:1001-1097)
5a: SCOP_d2ny4d1 (D:3001-3128)
6a: SCOP_d2ny4c1 (C:2001-2111)
7a: SCOP_d2ny4a1 (A:83-491)
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Classes
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)
(
)
Folds
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)
(
)
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
d2ny4d2
D:3129-3229
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d2ny4c2
C:2112-2214
Family
:
C2 set domains
(47)
Protein domain
:
CD4 C2-set domains
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
3a
d2ny4b2
B:1098-1181
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
CD4 V-set domains
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
4a
d2ny4b1
B:1001-1097
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Human (Homo sapiens), cluster 1 [TaxId: 9606]
(37)
5a
d2ny4d1
D:3001-3128
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
(31)
6a
d2ny4c1
C:2001-2111
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
d2ny4a1
A:83-491
[
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CATH Domains
(2, 7)
Info
all CATH domains
1a: CATH_2ny4A00 (A:83-491)
2a: CATH_2ny4C02 (C:2111-2213)
2b: CATH_2ny4C01 (C:2001-2110)
2c: CATH_2ny4D02 (D:3129-3228)
2d: CATH_2ny4D01 (D:3001-3128)
2e: CATH_2ny4B01 (B:1001-1098)
2f: CATH_2ny4B02 (B:1099-1173)
View:
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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. Strain: hxbc2.
(5)
1a
2ny4A00
A:83-491
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: hxbc2.
(13)
2a
2ny4C02
C:2111-2213
2b
2ny4C01
C:2001-2110
2c
2ny4D02
D:3129-3228
2d
2ny4D01
D:3001-3128
2e
2ny4B01
B:1001-1098
2f
2ny4B02
B:1099-1173
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_C2_set_2ny4B01 (B:1100-1178)
2a: PFAM_V_set_2ny4B02 (B:1001-1105)
3a: PFAM_GP120_2ny4A01 (A:83-491)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C2-set
(18)
Homo sapiens (Human)
(18)
1a
C2-set-2ny4B01
B:1100-1178
Family
:
V-set
(144)
Homo sapiens (Human)
(61)
2a
V-set-2ny4B02
B:1001-1105
Clan
:
no clan defined [family: GP120]
(26)
Family
:
GP120
(26)
Human immunodeficiency virus type 1 group M subtype B (isolate MFA) (HIV-1)
(5)
3a
GP120-2ny4A01
A:83-491
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