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2P5W
Asym. Unit
Info
Asym.Unit (160 KB)
Biol.Unit 1 (152 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF HIGH AFFINITY HUMAN T-CELL RECEPTORS BOUND TO PMHC REVEAL NATIVE DIAGONAL BINDING GEOMETRY
Authors
:
M. Sami, P. J. Rizkallah, S. Dunn, Y. Li, R. Moysey, A. Vuidepot, E. Basto P. Todorov, P. Molloy, F. Gao, J. M. Boulter, B. K. Jakobsen
Date
:
16 Mar 07 (Deposition) - 25 Sep 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
T-Cell Receptor, Cdr2, Phage Display, Mutant, High Affinity, Ny-Eso- 1, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Sami, P. J. Rizkallah, S. Dunn, P. Molloy, R. Moysey, A. Vuidepot, E. Baston, P. Todorov, L. Yi, F. Gao, J. M. Boulter, B. K. Jakobsen
Crystal Structures Of High Affinity Human T-Cell Receptors Bound To Peptide Major Histocompatibility Complex Reveal Native Diagonal Binding Geometry
Protein Eng. Des. Sel. V. 20 397 2007
[
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Hetero Components
(5, 20)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
4a: MAGNESIUM ION (MGa)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
GOL
11
Ligand/Ion
GLYCEROL
4
MG
1
Ligand/Ion
MAGNESIUM ION
5
SO4
6
Ligand/Ion
SULFATE ION
[
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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)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (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_HUMAN
98-104
1
B:78-84
1A02_HUMAN
281-287
1
A:257-263
[
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]
Exons
(1, 1)
Info
All Exons
Exon 1.2c (C:1-9)
View:
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All Exon Boundaries
1: Boundary 1.2a/1.2c
2: Boundary 1.2c/-
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
1.1b
ENST00000328435
1b
ENSE00001657401
X:153847522-153847201
322
CTG1B_HUMAN
1-90
90
0
-
-
1.2a
ENST00000328435
2a
ENSE00001758669
X:153846529-153846395
135
CTG1B_HUMAN
90-135
46
0
-
-
1.2c
ENST00000328435
2c
ENSE00001800972
X:153846155-153845865
291
CTG1B_HUMAN
135-180
46
1
C:1-9
9
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2p5wb_ (B:)
2a: SCOP_d2p5wa1 (A:182-276)
3a: SCOP_d2p5wa2 (A:1-181)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
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
:
beta2-microglobulin
(530)
Human (Homo sapiens) [TaxId: 9606]
(350)
1a
d2p5wb_
B:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d2p5wa1
A:182-276
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
d2p5wa2
A:1-181
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2p5wA01 (A:1-181)
2a: CATH_2p5wB00 (B:0-99)
2b: CATH_2p5wA02 (A:182-270)
2c: CATH_2p5wD01 (D:1-114)
2d: CATH_2p5wE01 (E:0-112)
2e: CATH_2p5wE02 (E:113-238)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
2p5wA01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2p5wB00
B:0-99
2b
2p5wA02
A:182-270
2c
2p5wD01
D:1-114
2d
2p5wE01
E:0-112
2e
2p5wE02
E:113-238
[
close CATH info
]
Pfam Domains
(4, 5)
Info
all PFAM domains
1a: PFAM_C1_set_2p5wA01 (A:188-271)
1b: PFAM_C1_set_2p5wB01 (B:11-92)
2a: PFAM_MHC_I_2p5wA02 (A:1-179)
3a: PFAM_DUF1968_2p5wD01 (D:121-192)
4a: PFAM_Pcc1_2p5wC01 (C:1-9)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-2p5wA01
A:188-271
1b
C1-set-2p5wB01
B:11-92
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
2a
MHC_I-2p5wA02
A:1-179
Clan
:
no clan defined [family: DUF1968]
(16)
Family
:
DUF1968
(16)
Homo sapiens (Human)
(14)
3a
DUF1968-2p5wD01
D:121-192
Clan
:
no clan defined [family: Pcc1]
(3)
Family
:
Pcc1
(3)
Homo sapiens (Human)
(3)
4a
Pcc1-2p5wC01
C:1-9
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