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1N0X
Asym. Unit
Info
Asym.Unit (169 KB)
Biol.Unit 1 (162 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A BROADLY NEUTRALIZING ANTI-HIV-1 ANTIBODY IN COMPLEX WITH A PEPTIDE MIMOTOPE
Authors
:
E. O. Saphire, M. Montero, A. Menendez, M. B. Irving, M. B. Zwick, P. W. H. D. R. Burton, J. K. Scott, I. A. Wilson
Date
:
15 Oct 02 (Deposition) - 13 Apr 04 (Release) - 21 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : H,K,L,M,P,R
Biol. Unit 1: H,K,L,M,P,R (1x)
Keywords
:
Antibody-Peptide Complex, Peptide Dimer, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. O. Saphire, M. Montero, A. Menendez, M. B. Irving, M. B. Zwick, P. W. H. I. Parren, D. R. Burton, J. K. Scott, I. A. Wilson
Crystal Structure Of A Broadly Neutralizing Anti-Hiv-1 Antibody In Complex With A Peptide Mimotope
To Be Published
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Hetero Components
(5, 16)
Info
All Hetero Components
1a: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
3a: POTASSIUM ION (Ka)
4a: L-ORNITHINE (ORNa)
4b: L-ORNITHINE (ORNb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CXS
1
Ligand/Ion
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2
GOL
8
Ligand/Ion
GLYCEROL
3
K
1
Ligand/Ion
POTASSIUM ION
4
ORN
2
Mod. Amino Acid
L-ORNITHINE
5
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS P:1 , HOH P:197 , HIS R:1 , GLU R:2 , ARG R:3 , TYR R:5 , HOH R:916
BINDING SITE FOR RESIDUE SO4 R 901
02
AC2
SOFTWARE
SER L:59 , ASP L:60 , HOH R:917
BINDING SITE FOR RESIDUE SO4 R 902
03
AC3
SOFTWARE
ARG H:83 , SER H:84 , SER H:195 , SER H:196 , HOH H:1268
BINDING SITE FOR RESIDUE SO4 H 903
04
AC4
SOFTWARE
ARG K:83 , ALA K:85 , SER K:196 , HOH K:940 , HOH K:988
BINDING SITE FOR RESIDUE SO4 K 904
05
AC5
SOFTWARE
HIS P:1 , HIS R:1
BINDING SITE FOR RESIDUE K P 1001
06
AC6
SOFTWARE
TYR H:98 , TRP H:100 , ASP H:100B , PRO H:100D , HOH H:1387 , SER M:14 , PRO M:15 , GLU M:17 , ARG M:106 , HOH M:892 , HOH M:966 , ARG R:13
BINDING SITE FOR RESIDUE CXS H 1201
07
AC7
SOFTWARE
ASN K:31 , PHE K:32 , VAL K:33 , VAL K:95 , TYR K:98 , ASN K:100G , TYR K:100H
BINDING SITE FOR RESIDUE GOL K 801
08
AC8
SOFTWARE
LYS H:228 , SER L:121 , ASP L:122 , GLU L:123
BINDING SITE FOR RESIDUE GOL L 803
09
AC9
SOFTWARE
PRO M:8 , GLY M:9 , THR M:10
BINDING SITE FOR RESIDUE GOL M 804
10
BC1
SOFTWARE
SER K:7 , GLY K:8
BINDING SITE FOR RESIDUE GOL K 805
11
BC2
SOFTWARE
TYR K:53 , ASN K:54 , HOH K:1064 , ARG L:18 , THR L:76
BINDING SITE FOR RESIDUE GOL K 806
12
BC3
SOFTWARE
TYR H:98 , SER H:99 , TRP H:100 , GLU M:17
BINDING SITE FOR RESIDUE GOL H 808
13
BC4
SOFTWARE
ILE H:51 , GLY H:55 , THR H:70 , ALA H:71
BINDING SITE FOR RESIDUE GOL H 809
14
BC5
SOFTWARE
ASP M:60 , HOH M:970
BINDING SITE FOR RESIDUE GOL M 800
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_066403 (W148R, chain L/M, )
2: VAR_003897 (V191L, chain L/M, )
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/M
W
148
R
2
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
L/M
V
191
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (L:192-198,M:192-198,H:206-212,K:20...)
;
View:
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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
2
L:192-198
M:192-198
IGG1_HUMAN
200-206
425-431
2
H:206-212
K:206-212
-
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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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1n0xh2 (H:114-228)
1b: SCOP_d1n0xk2 (K:114-230)
2a: SCOP_d1n0xl2 (L:108-214)
2b: SCOP_d1n0xm2 (M:108-214)
3a: SCOP_d1n0xh1 (H:1-113)
3b: SCOP_d1n0xk1 (K:1-113)
4a: SCOP_d1n0xl1 (L:1-107)
4b: SCOP_d1n0xm1 (M:1-107)
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(
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Superfamilies
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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
d1n0xh2
H:114-228
1b
d1n0xk2
K:114-230
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1n0xl2
L:108-214
2b
d1n0xm2
M: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
d1n0xh1
H:1-113
3b
d1n0xk1
K:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.1 [TaxId: 9606]
(8)
4a
d1n0xl1
L:1-107
4b
d1n0xm1
M:1-107
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1n0xL02 (L:108-211)
1b: CATH_1n0xL01 (L:1-107)
1c: CATH_1n0xM01 (M:1-107)
1d: CATH_1n0xK02 (K:110-230)
1e: CATH_1n0xH02 (H:110-228)
1f: CATH_1n0xH01 (H:1-109)
1g: CATH_1n0xK01 (K:1-109)
1h: CATH_1n0xM02 (M:108-211)
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(
)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
1n0xL02
L:108-211
1b
1n0xL01
L:1-107
1c
1n0xM01
M:1-107
1d
1n0xK02
K:110-230
1e
1n0xH02
H:110-228
1f
1n0xH01
H:1-109
1g
1n0xK01
K:1-109
1h
1n0xM02
M:108-211
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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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Asymmetric Unit 1
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