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3HI1
Asym. Unit
Info
Asym.Unit (510 KB)
Biol.Unit 1 (497 KB)
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(1)
Title
:
STRUCTURE OF HIV-1 GP120 (CORE WITH V3) IN COMPLEX WITH CD4-BINDING-SITE ANTIBODY F105
Authors
:
Y. D. Kwon, L. Chen, T. Zhou, X. Wu, S. O'Dell, L. Cavacini, A. J. Hessell, M. Pancera, M. Tang, L. Xu, Z. Yang, M. -Y. Zhang, J. Arthos, D. R. Burton D. Dimitrov, G. J. Nabel, M. Posner, J. Sodroski, R. Wyatt, J. R. Mascol P. D. Kwong
Date
:
18 May 09 (Deposition) - 17 Nov 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,G,H,J,L
Biol. Unit 1: A,B,G,H,J,L (1x)
Keywords
:
Hiv, Gp120, Cd4 Binding Site Antibody, F105, Immune Evasion, Aids, Apoptosis, Cell Membrane, Cleavage On Pair Of Basic Residues, Disulfide Bond, Envelope Protein, Fusion Protein, Glycoprotein, Host-Virus Interaction, Lipoprotein, Membrane, Palmitate, Transmembrane, Viral Immunoevasion, Virion, Structural Protein- Immune System Complex
(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
(1, 27)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
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)
1n: N-ACETYL-D-GLUCOSAMINE (NAGn)
1o: N-ACETYL-D-GLUCOSAMINE (NAGo)
1p: N-ACETYL-D-GLUCOSAMINE (NAGp)
1q: N-ACETYL-D-GLUCOSAMINE (NAGq)
1r: N-ACETYL-D-GLUCOSAMINE (NAGr)
1s: N-ACETYL-D-GLUCOSAMINE (NAGs)
1t: N-ACETYL-D-GLUCOSAMINE (NAGt)
1u: N-ACETYL-D-GLUCOSAMINE (NAGu)
1v: N-ACETYL-D-GLUCOSAMINE (NAGv)
1w: N-ACETYL-D-GLUCOSAMINE (NAGw)
1x: N-ACETYL-D-GLUCOSAMINE (NAGx)
1y: N-ACETYL-D-GLUCOSAMINE (NAGy)
1z: N-ACETYL-D-GLUCOSAMINE (NAGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
27
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(27, 27)
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)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN G:234 , THR G:236 , PRO G:238
BINDING SITE FOR RESIDUE NAG G 734
02
AC2
SOFTWARE
LYS G:231 , THR G:240 , ASN G:241
BINDING SITE FOR RESIDUE NAG G 741
03
AC3
SOFTWARE
PRO G:212 , ASN G:262 , CYS G:445 , SER G:446 , SER G:447
BINDING SITE FOR RESIDUE NAG G 762
04
AC4
SOFTWARE
ASN G:276 , THR G:278 , ASN G:279
BINDING SITE FOR RESIDUE NAG G 776
05
AC5
SOFTWARE
GLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLU G:290 , GLN G:344 , LYS G:348
BINDING SITE FOR RESIDUE NAG G 789
06
AC6
SOFTWARE
HOH G:53 , ASN G:295 , NAG G:832
BINDING SITE FOR RESIDUE NAG G 795
07
AC7
SOFTWARE
ARG G:298 , ASN G:300 , ASN G:301 , GLN G:422
BINDING SITE FOR RESIDUE NAG G 801
08
AC8
SOFTWARE
HIS G:330 , ASN G:332 , NAG G:795
BINDING SITE FOR RESIDUE NAG G 832
09
AC9
SOFTWARE
ASN G:356 , LYS G:357 , GLY G:464
BINDING SITE FOR RESIDUE NAG G 856
10
BC1
SOFTWARE
ASN G:386 , THR G:388
BINDING SITE FOR RESIDUE NAG G 886
11
BC2
SOFTWARE
ASN G:394 , ASP G:395
BINDING SITE FOR RESIDUE NAG G 894
12
BC3
SOFTWARE
LEU G:265 , ASN G:448
BINDING SITE FOR RESIDUE NAG G 948
13
BC4
SOFTWARE
ASN G:463
BINDING SITE FOR RESIDUE NAG G 963
14
BC5
SOFTWARE
ASN J:234 , THR J:236 , PRO J:238
BINDING SITE FOR RESIDUE NAG J 734
15
BC6
SOFTWARE
ASN J:241
BINDING SITE FOR RESIDUE NAG J 741
16
BC7
SOFTWARE
PRO J:212 , VAL J:254 , ASN J:262 , ARG J:444 , CYS J:445 , SER J:446 , SER J:447 , NAG J:948
BINDING SITE FOR RESIDUE NAG J 762
17
BC8
SOFTWARE
ASN J:276 , THR J:278 , ASN J:279
BINDING SITE FOR RESIDUE NAG J 776
18
BC9
SOFTWARE
GLU J:268 , GLU J:269 , ILE J:270 , ASN J:289 , GLN J:344
BINDING SITE FOR RESIDUE NAG J 789
19
CC1
SOFTWARE
ASN J:295 , NAG J:913
BINDING SITE FOR RESIDUE NAG J 795
20
CC2
SOFTWARE
PRO J:299 , ASN J:301
BINDING SITE FOR RESIDUE NAG J 801
21
CC3
SOFTWARE
ASN J:295 , ARG J:327 , ASN J:332 , THR J:415 , NAG J:913
BINDING SITE FOR RESIDUE NAG J 832
22
CC4
SOFTWARE
ASN J:356
BINDING SITE FOR RESIDUE NAG J 856
23
CC5
SOFTWARE
ASN J:386 , THR J:388
BINDING SITE FOR RESIDUE NAG J 886
24
CC6
SOFTWARE
ASN J:394
BINDING SITE FOR RESIDUE NAG J 894
25
CC7
SOFTWARE
ARG J:412 , ASN J:413 , NAG J:795 , NAG J:832
BINDING SITE FOR RESIDUE NAG J 913
26
CC8
SOFTWARE
SER J:446 , SER J:447 , ASN J:448 , NAG J:762
BINDING SITE FOR RESIDUE NAG J 948
27
CC9
SOFTWARE
THR J:462 , ASN J:463
BINDING SITE FOR RESIDUE NAG J 963
[
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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
;
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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, 6)
Info
All SCOP Domains
1a: SCOP_d3hi1a1 (A:1-107)
1b: SCOP_d3hi1l1 (L:1-107)
2a: SCOP_d3hi1a2 (A:108-214)
2b: SCOP_d3hi1l2 (L:108-214)
3a: SCOP_d3hi1g_ (G:)
3b: SCOP_d3hi1j_ (J:)
View:
Select:
Label:
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
d3hi1a1
A:1-107
1b
d3hi1l1
L:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
2a
d3hi1a2
A:108-214
2b
d3hi1l2
L:108-214
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
d3hi1g_
G:
3b
d3hi1j_
J:
[
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]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3hi1A02 (A:109-211)
1b: CATH_3hi1L02 (L:109-211)
1c: CATH_3hi1B02 (B:114-212)
1d: CATH_3hi1H02 (H:114-212)
1e: CATH_3hi1B01 (B:1-113)
1f: CATH_3hi1H01 (H:1-113)
View:
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Hiv-1 (Human immunodeficiency virus type 1)
(1)
1a
3hi1A02
A:109-211
1b
3hi1L02
L:109-211
1c
3hi1B02
B:114-212
1d
3hi1H02
H:114-212
1e
3hi1B01
B:1-113
1f
3hi1H01
H:1-113
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
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all
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Protein
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain G
Chain H
Chain J
Chain L
Asymmetric Unit 1
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