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1RZJ
Biol. Unit 1
Info
Asym.Unit (173 KB)
Biol.Unit 1 (165 KB)
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(1)
Title
:
HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B
Authors
:
C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, M. Farzan, P. D. Kwong
Date
:
24 Dec 03 (Deposition) - 03 Feb 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : C,G,H,L
Biol. Unit 1: C,G,H,L (1x)
Keywords
:
Complex (Hiv Envelope Protein-Cd4-Fab); Hiv-1 Exterior Envelope Gp120 From Laboratory-Adapted Isolate; Hxbc2; Surface T-Cell Glycoprotein Cd4; Antigen-Binding Fragment Of Human Immunoglobulin 17B, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, H. Choe, M. Farzan, P. D. Kwong
Structural Basis Of Tyrosine Sulfation And Vh-Gene Usage In Antibodies That Recognize The Hiv Type 1 Coreceptor-Binding Site On Gp120
Proc. Natl. Acad. Sci. Usa V. 101 2706 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 17)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
1b: ALPHA-L-FUCOSE (FUCb)
2a: ISOPROPYL ALCOHOL (IPAa)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
4b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
4c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
2
IPA
1
Ligand/Ion
ISOPROPYL ALCOHOL
3
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
3
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
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Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN G:88 , VAL G:89
BINDING SITE FOR RESIDUE NDG G 588
02
AC2
SOFTWARE
VAL G:127 , ASN G:197
BINDING SITE FOR RESIDUE NAG G 697
03
AC3
SOFTWARE
ASN G:230 , THR G:232 , PRO G:238 , CYS G:239 , THR G:240 , ASN G:241 , NAG G:734 , HOH G:1080
BINDING SITE FOR RESIDUE NDG G 730
04
AC4
SOFTWARE
PHE G:233 , ASN G:234 , THR G:236 , PRO G:238 , NDG G:730 , HOH G:1075 , HOH G:1121 , GLU L:195
BINDING SITE FOR RESIDUE NAG G 734
05
AC5
SOFTWARE
ASN G:241
BINDING SITE FOR RESIDUE NDG G 741
06
AC6
SOFTWARE
ARG G:252 , ASN G:262 , SER G:446 , SER G:447 , NAG G:948 , HOH G:1135 , THR L:56
BINDING SITE FOR RESIDUE NAG G 762
07
AC7
SOFTWARE
ASN G:276 , THR G:278 , ASP G:279 , ASN L:210
BINDING SITE FOR RESIDUE NAG G 776
08
AC8
SOFTWARE
GLU G:268 , GLU G:269 , VAL G:270 , ASN G:289 , GLN G:344
BINDING SITE FOR RESIDUE NAG G 789
09
AC9
SOFTWARE
ASN G:339 , LYS G:343 , TRP G:395 , HOH G:1116
BINDING SITE FOR RESIDUE NAG G 839
10
BC1
SOFTWARE
ASN G:386 , THR G:388 , GLN G:389
BINDING SITE FOR RESIDUE NAG G 886
11
BC2
SOFTWARE
ASN G:392
BINDING SITE FOR RESIDUE NAG G 892
12
BC3
SOFTWARE
SER G:291 , GLU G:293 , SER G:446 , ASN G:448 , NAG G:762 , HOH G:1058 , GLU H:1 , THR L:56
BINDING SITE FOR RESIDUE NAG G 948
13
BC4
SOFTWARE
GLU G:293 , ASN G:295 , ASN G:332 , FUC G:796 , HOH G:1089 , ASP H:27
BINDING SITE FOR RESIDUE NAG G 795
14
BC5
SOFTWARE
ARG G:444 , NAG G:795 , GLU H:1 , VAL H:95 , TYR H:96 , LYS H:101 , HIS H:102
BINDING SITE FOR RESIDUE FUC G 796
15
BC6
SOFTWARE
SER G:461 , ASN G:463 , FUC G:964 , HOH G:1069
BINDING SITE FOR RESIDUE NAG G 963
16
BC7
SOFTWARE
NAG G:963
BINDING SITE FOR RESIDUE FUC G 964
17
BC8
SOFTWARE
VAL G:255 , PHE G:376 , PHE G:382 , HOH G:1008
BINDING SITE FOR RESIDUE IPA G 1000
[
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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
;
View:
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(7, 7)
Info
All SCOP Domains
1a: SCOP_d1rzjh2 (H:114-214)
2a: SCOP_d1rzjl2 (L:110-212)
3a: SCOP_d1rzjc2 (C:98-181)
4a: SCOP_d1rzjc1 (C:1-97)
5a: SCOP_d1rzjh1 (H:1-113)
6a: SCOP_d1rzjl1 (L:1-109)
7a: SCOP_d1rzjg_ (G:)
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)
(
)
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)
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)
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)
(
)
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)
(
)
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
d1rzjh2
H:114-214
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1rzjl2
L:110-212
Family
:
C2 set domains
(47)
Protein domain
:
CD4 C2-set domains
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
3a
d1rzjc2
C:98-181
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
CD4 V-set domains
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
4a
d1rzjc1
C:1-97
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Human (Homo sapiens), cluster 1 [TaxId: 9606]
(37)
5a
d1rzjh1
H:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
(31)
6a
d1rzjl1
L:1-109
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
d1rzjg_
G:
[
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]
CATH Domains
(2, 7)
Info
all CATH domains
1a: CATH_1rzjG00 (G:83-492)
2a: CATH_1rzjL02 (L:109-211)
2b: CATH_1rzjC01 (C:1-98)
2c: CATH_1rzjC02 (C:99-173)
2d: CATH_1rzjL01 (L:1-108)
2e: CATH_1rzjH02 (H:114-213)
2f: CATH_1rzjH01 (H:1-113)
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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: clade b. Variant: laboratory-adapted isolate hxbc2.
(3)
1a
1rzjG00
G:83-492
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: clade b. Variant: laboratory-adapted isolate hxbc2.
(3)
2a
1rzjL02
L:109-211
2b
1rzjC01
C:1-98
2c
1rzjC02
C:99-173
2d
1rzjL01
L:1-108
2e
1rzjH02
H:114-213
2f
1rzjH01
H:1-113
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_C2_set_1rzjC01 (C:100-178)
2a: PFAM_V_set_1rzjC02 (C:1-105)
3a: PFAM_GP120_1rzjG01 (G:195-492)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C2-set
(18)
Homo sapiens (Human)
(18)
1a
C2-set-1rzjC01
C:100-178
Family
:
V-set
(144)
Homo sapiens (Human)
(61)
2a
V-set-1rzjC02
C:1-105
Clan
:
no clan defined [family: GP120]
(26)
Family
:
GP120
(26)
Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1)
(2)
3a
GP120-1rzjG01
G:195-492
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Protein
Nucleic
Backbone
Sidechain
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Chain H
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Asymmetric Unit 1
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Asym.Unit (173 KB)
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Biol.Unit 1 (165 KB)
Header - Biol.Unit 1
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