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2QSC
Asym. Unit
Info
Asym.Unit (75 KB)
Biol.Unit 1 (69 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF ANTI-HIV-1 V3-FAB F425-B4E8 IN COMPLEX WITH A V3-PEPTIDE
Authors
:
C. H. Bell, A. Schiefner, R. L. Stanfield, I. A. Wilson
Date
:
30 Jul 07 (Deposition) - 15 Jan 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : H,L,P
Biol. Unit 1: H,L,P (1x)
Keywords
:
Fab-Peptide Complex, Hiv-1, Gp120, V3 Loop, Immunoglobulin Fold, Aids, Apoptosis, Envelope Protein, Fusion Protein, Glycoprotein, Host-Virus Interaction, Membrane, Transmembrane, Viral Immunoevasion, Virion, Immune System
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
C. H. Bell, R. Pantophlet, A. Schiefner, L. A. Cavacini, R. L. Stanfield, D. R. Burton, I. A. Wilson
Structure Of Antibody F425-B4E8 In Complex With A V3 Peptid Reveals A New Binding Mode For Hiv-1 Neutralization.
J. Mol. Biol. V. 375 969 2008
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CL
4
Ligand/Ion
CHLORIDE ION
3
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
ZN
4
Ligand/Ion
ZINC ION
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Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC5 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC8 (SOFTWARE)
08: AC9 (SOFTWARE)
09: AD1 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN H:28 , SER H:31 , NAG H:228
BINDING SITE FOR RESIDUE NAG H 227
02
AC3
SOFTWARE
NAG H:227 , BMA H:229
BINDING SITE FOR RESIDUE NAG H 228
03
AC4
SOFTWARE
NAG H:228
BINDING SITE FOR RESIDUE BMA H 229
04
AC5
SOFTWARE
HIS H:172 , THR H:192 , ASN L:137 , ASN L:138 , CL L:217
BINDING SITE FOR RESIDUE ZN L 215
05
AC6
SOFTWARE
GLN L:24 , HIS L:70 , HOH L:219
BINDING SITE FOR RESIDUE ZN L 216
06
AC7
SOFTWARE
ASN L:138 , ZN L:215
BINDING SITE FOR RESIDUE CL L 217
07
AC8
SOFTWARE
ASP H:53 , GLU H:55 , CL H:234
BINDING SITE FOR RESIDUE ZN H 230
08
AC9
SOFTWARE
GLU H:85 , CL H:232 , CL H:233 , GLU L:81
BINDING SITE FOR RESIDUE ZN H 231
09
AD1
SOFTWARE
ZN H:231 , GLU L:81
BINDING SITE FOR RESIDUE CL H 232
10
BC1
SOFTWARE
THR H:84 , ZN H:231 , GLU L:81
BINDING SITE FOR RESIDUE CL H 233
11
BC2
SOFTWARE
SER H:52 , ASP H:53 , THR H:56 , ZN H:230
BINDING SITE FOR RESIDUE CL H 234
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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:
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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:
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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
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All Exon Boundaries
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2qscl2 (L:108-214)
2a: SCOP_d2qscl1 (L:3-107)
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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 light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
1a
d2qscl2
L:108-214
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
(31)
2a
d2qscl1
L:3-107
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2qscL02 (L:108-211)
1b: CATH_2qscH02 (H:114-226)
1c: CATH_2qscH01 (H:1-113)
1d: CATH_2qscL01 (L:1-107)
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Organisms
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)
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)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
2qscL02
L:108-211
1b
2qscH02
H:114-226
1c
2qscH01
H:1-113
1d
2qscL01
L:1-107
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_GP120_2qscP01 (P:304-320)
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Clans
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)
Clan
:
no clan defined [family: GP120]
(26)
Family
:
GP120
(26)
Human immunodeficiency virus type 1 group M subtype B (isolate MN) (HIV-1)
(5)
1a
GP120-2qscP01
P:304-320
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Asymmetric Unit 1
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