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1T20
Asym. Unit
Info
Asym.Unit (75 KB)
Biol.Unit 1 (71 KB)
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(1)
Title
:
STRUCTURAL BASIS FOR DEGENERATE RECOGNITION OF HIV PEPTIDE VARIANTS BY CYTOTOXIC LYMPHOCYTE, VARIANT SL9-6I
Authors
:
E. Martinez-Hackert, N. Anikeeva, S. A. Kalams, B. D. Walker, W. A. Hendrickson, Y. Sykulev
Date
:
19 Apr 04 (Deposition) - 06 Sep 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Ctl, Cytotoxic T Lymphocytes, Hiv, Human Immunodeficiency Virus, Mhc, Major Histocompatibility Complex, Pmhc, Peptide Mhc Complex, Rmsd, Root-Mean-Squared Deviation, Siv, Simian Immunodeficiency Virus, Tcr, T-Cell Receptor, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Martinez-Hackert, N. Anikeeva, S. A. Kalams, B. D. Walker, W. A. Hendrickson, Y. Sykulev
Structural Basis For Degenerate Recognition Of Natural Hiv Peptide Variants By Cytotoxic Lymphocytes.
J. Biol. Chem. V. 281 20205 2006
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
Info
All Hetero Components
View:
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Label:
Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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]
SAPs(SNPs)/Variants
(22, 22)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004334 (F9Y, chain A, )
02: VAR_004335 (D30N, chain A, )
03: VAR_016726 (A41G, chain A, )
04: VAR_004336 (Q43R, chain A, )
05: VAR_004337 (K66N, chain A, )
06: VAR_016727 (H70Q, chain A, )
07: VAR_004338 (T73I, chain A, )
08: VAR_016728 (H74D, chain A, )
09: VAR_004339 (V95L, chain A, )
10: VAR_004340 (R97M, chain A, )
11: VAR_004341 (Y99C, chain A, )
12: VAR_004342 (Y99F, chain A, )
13: VAR_004343 (W107G, chain A, )
14: VAR_004344 (M138K, chain A, )
15: VAR_004345 (A149T, chain A, )
16: VAR_004346 (V152E, chain A, )
17: VAR_004348 (L156Q, chain A, )
18: VAR_004347 (L156W, chain A, )
19: VAR_004349 (T163E, chain A, )
20: VAR_016729 (E166D, chain A, )
21: VAR_016730 (W167G, chain A, )
22: VAR_004350 (A236E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_004334
F
33
Y
1A02_HUMAN
Polymorphism
---
A
F
9
Y
02
UniProt
VAR_004335
D
54
N
1A02_HUMAN
Polymorphism
---
A
D
30
N
03
UniProt
VAR_016726
A
65
G
1A02_HUMAN
Polymorphism
---
A
A
41
G
04
UniProt
VAR_004336
Q
67
R
1A02_HUMAN
Polymorphism
---
A
Q
43
R
05
UniProt
VAR_004337
K
90
N
1A02_HUMAN
Polymorphism
---
A
K
66
N
06
UniProt
VAR_016727
H
94
Q
1A02_HUMAN
Polymorphism
---
A
H
70
Q
07
UniProt
VAR_004338
T
97
I
1A02_HUMAN
Polymorphism
---
A
T
73
I
08
UniProt
VAR_016728
H
98
D
1A02_HUMAN
Polymorphism
---
A
H
74
D
09
UniProt
VAR_004339
V
119
L
1A02_HUMAN
Polymorphism
---
A
V
95
L
10
UniProt
VAR_004340
R
121
M
1A02_HUMAN
Polymorphism
---
A
R
97
M
11
UniProt
VAR_004341
Y
123
C
1A02_HUMAN
Polymorphism
---
A
Y
99
C
12
UniProt
VAR_004342
Y
123
F
1A02_HUMAN
Polymorphism
---
A
Y
99
F
13
UniProt
VAR_004343
W
131
G
1A02_HUMAN
Polymorphism
---
A
W
107
G
14
UniProt
VAR_004344
M
162
K
1A02_HUMAN
Polymorphism
---
A
M
138
K
15
UniProt
VAR_004345
A
173
T
1A02_HUMAN
Polymorphism
---
A
A
149
T
16
UniProt
VAR_004346
V
176
E
1A02_HUMAN
Polymorphism
---
A
V
152
E
17
UniProt
VAR_004348
L
180
Q
1A02_HUMAN
Polymorphism
---
A
L
156
Q
18
UniProt
VAR_004347
L
180
W
1A02_HUMAN
Polymorphism
---
A
L
156
W
19
UniProt
VAR_004349
T
187
E
1A02_HUMAN
Polymorphism
---
A
T
163
E
20
UniProt
VAR_016729
E
190
D
1A02_HUMAN
Polymorphism
---
A
E
166
D
21
UniProt
VAR_016730
W
191
G
1A02_HUMAN
Polymorphism
---
A
W
167
G
22
UniProt
VAR_004350
A
260
E
1A02_HUMAN
Polymorphism
---
A
A
236
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84,B:78-84,B:78-84,A:257-263)
;
View:
Select:
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.
B2MG_GORGO
98-104
1
B:78-84
B2MG_HUMAN
98-104
1
B:78-84
B2MG_PANTR
98-104
1
B:78-84
1A02_HUMAN
281-287
1
A:257-263
[
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Exons
(3, 3)
Info
All Exons
Exon 1.1a (B:1-3)
Exon 1.2a (B:3-96)
Exon 1.4 (B:96-99)
View:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2a
3: Boundary 1.2a/1.4
4: Boundary 1.4/1.5
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
1.1a
ENSPTRT00000012956
1a
ENSPTRE00000370636
chr15:
41860468-41860604
137
B2MG_PANTR
1-23
23
1
B:1-3
3
1.2a
ENSPTRT00000012956
2a
ENSPTRE00000238527
chr15:
41864413-41864691
279
B2MG_PANTR
23-116
94
1
B:3-96
94
1.4
ENSPTRT00000012956
4
ENSPTRE00000238528
chr15:
41865318-41865345
28
B2MG_PANTR
116-119
4
1
B:96-99
4
1.5
ENSPTRT00000012956
5
ENSPTRE00000070423
chr15:
41866598-41867140
543
B2MG_PANTR
-
0
0
-
-
[
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]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1t20b_ (B:)
2a: SCOP_d1t20a1 (A:182-275)
3a: SCOP_d1t20a2 (A:1-181)
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Folds
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Superfamilies
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(
)
Families
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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
:
beta2-microglobulin
(530)
Human (Homo sapiens) [TaxId: 9606]
(350)
1a
d1t20b_
B:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d1t20a1
A:182-275
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
Class I MHC, alpha-1 and alpha-2 domains
(294)
Human (Homo sapiens), HLA-A2.1 [TaxId: 9606]
(92)
3a
d1t20a2
A:1-181
[
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1t20A01 (A:1-181)
2a: CATH_1t20B00 (B:1-99)
2b: CATH_1t20A02 (A:182-270)
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Classes
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Architectures
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
(402)
Homologous Superfamily
:
Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1
(400)
Human (Homo sapiens)
(249)
1a
1t20A01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1t20B00
B:1-99
2b
1t20A02
A:182-270
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Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_C1_set_1t20A01 (A:188-271)
1b: PFAM_C1_set_1t20B01 (B:11-92)
2a: PFAM_MHC_I_1t20A02 (A:1-179)
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Organisms
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Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-1t20A01
A:188-271
1b
C1-set-1t20B01
B:11-92
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
2a
MHC_I-1t20A02
A:1-179
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Nucleic
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