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1G9M
Asym. Unit
Info
Asym.Unit (181 KB)
Biol.Unit 1 (172 KB)
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(1)
Title
:
HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B
Authors
:
P. D. Kwong, R. Wyatt, S. Majeed, J. Robinson, R. W. Sweet, J. Sodroski, W. A. Hendrickson
Date
:
24 Nov 00 (Deposition) - 27 Dec 00 (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
:
P. D. Kwong, R. Wyatt, S. Majeed, J. Robinson, R. W. Sweet, J. Sodroski, W. A. Hendrickson
Structures Of Hiv-1 Gp120 Envelope Glycoproteins From Laboratory-Adapted And Primary Isolates.
Structure Fold. Des. V. 8 1329 2000
(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
[
close Hetero Component info
]
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 , HOH G:1322
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
BINDING SITE FOR RESIDUE NDG G 730
04
AC4
SOFTWARE
PHE G:233 , ASN G:234 , THR G:236 , PRO G:238 , HOH G:1037 , HOH G:1076 , HOH G:1309 , HOH G:1324
BINDING SITE FOR RESIDUE NAG G 734
05
AC5
SOFTWARE
LEU G:86 , ASN G:229 , ASN G:241 , HOH G:1329
BINDING SITE FOR RESIDUE NDG G 741
06
AC6
SOFTWARE
ARG G:252 , ASN G:262 , SER G:446 , SER G:447 , HOH G:1045 , HOH G:1293 , THR L:56
BINDING SITE FOR RESIDUE NAG G 762
07
AC7
SOFTWARE
ASN G:276 , THR G:278 , ASP G:279 , HOH G:1145 , HOH G:1299 , HOH G:1308 , ASN L:212
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 , HOH G:1132 , HOH G:1311
BINDING SITE FOR RESIDUE NAG G 789
09
AC9
SOFTWARE
GLU G:293 , ASN G:295 , ASN G:332 , SER G:334 , FUC G:796 , HOH G:1077 , HOH G:1123 , HOH G:1326 , GLN H:1 , ASP H:27 , TYR H:100 , HOH H:341 , HOH H:452
BINDING SITE FOR RESIDUE NAG G 795
10
BC1
SOFTWARE
ARG G:444 , NAG G:795 , GLN H:1 , TYR H:100 , LYS H:116 , HIS H:117
BINDING SITE FOR RESIDUE FUC G 796
11
BC2
SOFTWARE
ASN G:339 , LYS G:343 , TRP G:395 , HOH G:1162
BINDING SITE FOR RESIDUE NAG G 839
12
BC3
SOFTWARE
ASN G:386 , THR G:388 , GLN G:389
BINDING SITE FOR RESIDUE NAG G 886
13
BC4
SOFTWARE
ASN G:392 , HOH G:1187 , HOH G:1193 , HOH G:1328
BINDING SITE FOR RESIDUE NAG G 892
14
BC5
SOFTWARE
SER G:291 , SER G:446 , ASN G:448 , HOH G:1157 , HOH G:1292 , HOH G:1330 , GLN H:1
BINDING SITE FOR RESIDUE NAG G 948
15
BC6
SOFTWARE
ASN G:463 , FUC G:964
BINDING SITE FOR RESIDUE NAG G 963
16
BC7
SOFTWARE
NAG G:963 , HOH G:1239
BINDING SITE FOR RESIDUE FUC G 964
17
BC8
SOFTWARE
SER G:375 , PHE G:376 , PHE G:382 , HOH G:1111
BINDING SITE FOR RESIDUE IPA G 1000
[
close Site info
]
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:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(4, 4)
Info
All Exons
Exon 1.3 (C:1-47)
Exon 1.4 (C:47-100)
Exon 1.5 (C:100-178)
Exon 1.6b (C:178-181)
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
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
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:100-178
79
1.6b
ENST00000011653
6b
ENSE00000716048
chr12:
6925222-6925569
348
CD4_HUMAN
203-319
117
1
C:178-181
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
-
-
[
close EXON info
]
SCOP Domains
(7, 7)
Info
All SCOP Domains
1a: SCOP_d1g9mh2 (H:130-229)
2a: SCOP_d1g9ml2 (L:110-214)
3a: SCOP_d1g9mc2 (C:98-181)
4a: SCOP_d1g9mc1 (C:1-97)
5a: SCOP_d1g9mh1 (H:1-129)
6a: SCOP_d1g9ml1 (L:1-109)
7a: SCOP_d1g9mg_ (G:)
View:
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)
(
)
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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
d1g9mh2
H:130-229
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1g9ml2
L:110-214
Family
:
C2 set domains
(47)
Protein domain
:
CD4 C2-set domains
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
3a
d1g9mc2
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
d1g9mc1
C:1-97
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Human (Homo sapiens), cluster 1 [TaxId: 9606]
(37)
5a
d1g9mh1
H:1-129
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
(31)
6a
d1g9ml1
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
d1g9mg_
G:
[
close SCOP info
]
CATH Domains
(2, 7)
Info
all CATH domains
1a: CATH_1g9mG00 (G:83-492)
2a: CATH_1g9mL02 (L:111-213)
2b: CATH_1g9mH01 (H:1-128)
2c: CATH_1g9mC01 (C:1-98)
2d: CATH_1g9mC02 (C:99-173)
2e: CATH_1g9mL01 (L:1-110)
2f: CATH_1g9mH02 (H:129-228)
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(
)
(
)
Architectures
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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
1g9mG00
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
1g9mL02
L:111-213
2b
1g9mH01
H:1-128
2c
1g9mC01
C:1-98
2d
1g9mC02
C:99-173
2e
1g9mL01
L:1-110
2f
1g9mH02
H:129-228
[
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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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Chain C
Chain G
Chain H
Chain L
Asymmetric Unit 1
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Asym.Unit (181 KB)
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