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3BHB
Asym. Unit
Info
Asym.Unit (71 KB)
Biol.Unit 1 (68 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF KMD PHOSPHOPEPTIDE BOUND TO HUMAN CLASS I MHC HLA-A2
Authors
:
F. Mohammed, M. Cobbold, A. L. Zarling, M. Salim, G. A. Barrett-Wilt, J. Shabanowitz, D. F. Hunt, V. H. Engelhard, B. E. Willcox
Date
:
28 Nov 07 (Deposition) - 21 Oct 08 (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
:
Phosphoserine, Phosphopeptide, Mhc, Hla-A2, Anchor Residue, Tumor Antigen, Glycoprotein, Host-Virus Interaction, Immune Response, Mhc I, Polymorphism, Transmembrane, Ubl Conjugation, Immunoglobulin Domain, Phosphoprotein, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Mohammed, M. Cobbold, A. L. Zarling, M. Salim, G. A. Barrett-Wilt, J. Shabanowitz, D. F. Hunt, V. H. Engelhard, B. E. Willcox
Phosphorylation-Dependent Interaction Between Antigenic Peptides And Mhc Class I: A Molecular Basis For The Presentation Of Transformed Self
Nat. Immunol. V. 9 1236 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
2a: PHOSPHOSERINE (SEPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
2
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP A:204 , LEU A:206 , ARG A:234 , GLN A:242 , HOH A:340 , SER B:11 , HIS B:13 , PRO B:14
BINDING SITE FOR RESIDUE EDO A 275
[
close Site info
]
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
[
close PROSITE info
]
Exons
(1, 1)
Info
All Exons
Exon 1.5b (C:1-10)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.5b
2: Boundary 1.5b/1.6
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
ENST00000261435
1a
ENSE00002042060
chr4:
40058446-40058650
205
N4BP2_HUMAN
-
0
0
-
-
1.2
ENST00000261435
2
ENSE00001489911
chr4:
40075075-40075171
97
N4BP2_HUMAN
-
0
0
-
-
1.3
ENST00000261435
3
ENSE00001077370
chr4:
40098847-40099189
343
N4BP2_HUMAN
1-77
77
0
-
-
1.5b
ENST00000261435
5b
ENSE00001077368
chr4:
40103695-40104838
1144
N4BP2_HUMAN
77-458
382
1
C:1-10
10
1.6
ENST00000261435
6
ENSE00001077366
chr4:
40108520-40108644
125
N4BP2_HUMAN
458-500
43
0
-
-
1.7
ENST00000261435
7
ENSE00001077374
chr4:
40113704-40113792
89
N4BP2_HUMAN
500-529
30
0
-
-
1.8
ENST00000261435
8
ENSE00001077367
chr4:
40115052-40115128
77
N4BP2_HUMAN
530-555
26
0
-
-
1.9
ENST00000261435
9
ENSE00001077378
chr4:
40119489-40119644
156
N4BP2_HUMAN
555-607
53
0
-
-
1.10
ENST00000261435
10
ENSE00001077376
chr4:
40121552-40123929
2378
N4BP2_HUMAN
607-1400
794
0
-
-
1.11
ENST00000261435
11
ENSE00001077380
chr4:
40124747-40124832
86
N4BP2_HUMAN
1400-1428
29
0
-
-
1.12
ENST00000261435
12
ENSE00001077375
chr4:
40125780-40125825
46
N4BP2_HUMAN
1429-1444
16
0
-
-
1.13
ENST00000261435
13
ENSE00001077373
chr4:
40127754-40127950
197
N4BP2_HUMAN
1444-1509
66
0
-
-
1.14
ENST00000261435
14
ENSE00001077371
chr4:
40133421-40133539
119
N4BP2_HUMAN
1510-1549
40
0
-
-
1.15
ENST00000261435
15
ENSE00001035498
chr4:
40138564-40138702
139
N4BP2_HUMAN
1549-1595
47
0
-
-
1.16a
ENST00000261435
16a
ENSE00001035492
chr4:
40144293-40144481
189
N4BP2_HUMAN
1596-1658
63
0
-
-
1.17
ENST00000261435
17
ENSE00001035489
chr4:
40146252-40146420
169
N4BP2_HUMAN
1659-1715
57
0
-
-
1.18
ENST00000261435
18
ENSE00001035496
chr4:
40154400-40154523
124
N4BP2_HUMAN
1715-1756
42
0
-
-
1.19c
ENST00000261435
19c
ENSE00001860132
chr4:
40155812-40159872
4061
N4BP2_HUMAN
1756-1770
15
0
-
-
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3bhbb_ (B:)
2a: SCOP_d3bhba1 (A:182-274)
3a: SCOP_d3bhba2 (A:1-181)
View:
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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
d3bhbb_
B:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d3bhba1
A:182-274
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
d3bhba2
A:1-181
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_3bhbA01 (A:1-181)
2a: CATH_3bhbB00 (B:2-99)
2b: CATH_3bhbA02 (A:182-270)
View:
Select:
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
3bhbA01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
3bhbB00
B:2-99
2b
3bhbA02
A:182-270
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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(currently selected atoms:
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Protein & NOT PROSITE
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Chain C
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Asym.Unit (71 KB)
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