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2NY7
Asym. Unit
Info
Asym.Unit (271 KB)
Biol.Unit 1 (262 KB)
Biol.Unit 2 (519 KB)
Biol.Unit 3 (519 KB)
Biol.Unit 4 (519 KB)
Biol.Unit 5 (519 KB)
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(1)
Title
:
HIV-1 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH THE BROADLY NEUTRALIZING CD4-BINDING-SITE ANTIBODY B12
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
:
2.30
Chains
:
Asym. Unit : G,H,L
Biol. Unit 1: G,H,L (1x)
Biol. Unit 2: G,H,L (2x)
Biol. Unit 3: G,H,L (2x)
Biol. Unit 4: G,H,L (2x)
Biol. Unit 5: G,H,L (2x)
Keywords
:
Hiv, Gp120, Broadly Neutralizing Antibody, B12, 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
(1, 13)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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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
ASN G:234 , THR G:236 , GLY G:237 , HOH G:1025
BINDING SITE FOR RESIDUE NAG G 734
02
AC2
SOFTWARE
VAL G:85 , ASN G:229 , ASN G:241
BINDING SITE FOR RESIDUE NAG G 741
03
AC3
SOFTWARE
ARG G:252 , ASN G:262 , PHE G:376 , ASN G:377 , CYS G:378 , SER G:446 , SER G:447 , HOH G:998
BINDING SITE FOR RESIDUE NAG G 762
04
AC4
SOFTWARE
ASN G:276 , ASP G:279 , HOH G:1030
BINDING SITE FOR RESIDUE NAG G 776
05
AC5
SOFTWARE
GLU G:268 , GLU G:269 , VAL G:270 , ASN G:289 , THR G:290 , GLN G:344
BINDING SITE FOR RESIDUE NAG G 789
06
AC6
SOFTWARE
ASN G:295 , ALA G:334
BINDING SITE FOR RESIDUE NAG G 795
07
AC7
SOFTWARE
ARG G:335 , ASN G:339 , TRP G:400
BINDING SITE FOR RESIDUE NAG G 839
08
AC8
SOFTWARE
PHE G:353 , GLY G:354 , ASN G:356 , LYS G:357 , ASN G:463 , HOH G:992
BINDING SITE FOR RESIDUE NAG G 856
09
AC9
SOFTWARE
ASN G:386 , THR G:388 , HOH G:975 , HOH G:989 , TRP H:100 , HOH H:300
BINDING SITE FOR RESIDUE NAG G 886
10
BC1
SOFTWARE
ASN G:392
BINDING SITE FOR RESIDUE NAG G 892
11
BC2
SOFTWARE
ILE G:360 , THR G:394 , ASN G:397 , SER G:398 , HOH G:1050 , GLY H:15
BINDING SITE FOR RESIDUE NAG G 897
12
BC3
SOFTWARE
ASN G:262 , SER G:291 , ASN G:448 , HOH G:1033
BINDING SITE FOR RESIDUE NAG G 948
13
BC4
SOFTWARE
ASN G:463 , HOH G:991 , LYS H:13
BINDING SITE FOR RESIDUE NAG G 963
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_066403 (W148R, chain L, )
2: VAR_003897 (V191L, chain L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_066403
W
40
R
IGKC_HUMAN
Disease (IGKCD)
---
L
W
148
R
2
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
L
V
191
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (L:192-198)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_HUMAN
85-91
1
L:192-198
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Exons
(0, 0)
Info
All Exons
View:
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Label:
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
(5, 5)
Info
All SCOP Domains
1a: SCOP_d2ny7h2 (H:114-230)
2a: SCOP_d2ny7l2 (L:108-214)
3a: SCOP_d2ny7h1 (H:1-113)
4a: SCOP_d2ny7l1 (L:1-107)
5a: SCOP_d2ny7g_ (G:)
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)
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Protein Domains
(
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(
)
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
d2ny7h2
H:114-230
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d2ny7l2
L:108-214
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Human (Homo sapiens), cluster 1 [TaxId: 9606]
(37)
3a
d2ny7h1
H:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.1 [TaxId: 9606]
(8)
4a
d2ny7l1
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
:
automated matches
(5)
Human immunodeficiency virus 1 [TaxId: 11676]
(4)
5a
d2ny7g_
G:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2ny7L02 (L:108-211)
1b: CATH_2ny7L01 (L:1-107)
1c: CATH_2ny7H02 (H:110-230)
1d: CATH_2ny7H01 (H:1-109)
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Architectures
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Topologies
(
)
(
)
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
2ny7L02
L:108-211
1b
2ny7L01
L:1-107
1c
2ny7H02
H:110-230
1d
2ny7H01
H:1-109
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_GP120_2ny7G01 (G:83-492)
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: GP120]
(26)
Family
:
GP120
(26)
Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1)
(2)
1a
GP120-2ny7G01
G:83-492
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Chain L
Asymmetric Unit 1
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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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Asym.Unit (271 KB)
Header - Asym.Unit
Biol.Unit 1 (262 KB)
Header - Biol.Unit 1
Biol.Unit 2 (519 KB)
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Biol.Unit 3 (519 KB)
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Biol.Unit 4 (519 KB)
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