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2X4R
Asym. Unit
Info
Asym.Unit (287 KB)
Biol.Unit 1 (140 KB)
Biol.Unit 2 (139 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MHC CLASS I HLA-A2.1 BOUND TO CYTOMEGALOVIRUS (CMV) PP65 EPITOPE
Authors
:
P. H. N. Celie, M. Toebes, B. Rodenko, H. Ovaa, A. Perrakis, T. N. M. Schumacher
Date
:
02 Feb 10 (Deposition) - 02 Mar 10 (Release) - 02 Mar 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: D,E,F (1x)
Biol. Unit 2: A,B,C (1x)
Keywords
:
Immunoglobulin Domain, Host-Virus Interaction, Glycation, Amyloidosis, Amyloid, Photocleavable Peptide, Immune Response, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. H. N. Celie, M. Toebes, B. Rodenko, H. Ovaa, A. Perrakis, T. N. M. Schumacher
Uv-Induced Ligand Exchange In Mhc Class I Protein Crystals.
J. Am. Chem. Soc. V. 131 12298 2009
[
close entry info
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Hetero Components
(1, 9)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
9
Ligand/Ion
GLYCEROL
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN E:8 , VAL E:9 , LYS E:94 , ASP E:96 , MET E:99 , HOH E:2060
BINDING SITE FOR RESIDUE GOL E1100
2
AC2
SOFTWARE
ARG D:97 , HIS D:114 , TRP D:147 , LEU D:156 , VAL F:3 , MET F:5 , VAL F:6 , ALA F:7 , HOH F:2002
BINDING SITE FOR RESIDUE GOL F1010
3
AC3
SOFTWARE
LEU D:206 , ARG D:234 , GLN D:242 , TYR E:10 , SER E:11 , PRO E:14 , HOH E:2018 , HOH E:2061
BINDING SITE FOR RESIDUE GOL E1101
4
AC4
SOFTWARE
MET D:98 , SER E:57 , LYS E:58 , TRP E:60 , GOL E:1103
BINDING SITE FOR RESIDUE GOL E1102
5
AC5
SOFTWARE
ARG D:6 , LYS E:58 , GOL E:1102
BINDING SITE FOR RESIDUE GOL E1103
6
AC6
SOFTWARE
ARG D:6 , PHE D:8 , TYR D:27 , ASP D:29 , ASP D:30 , HOH D:2115
BINDING SITE FOR RESIDUE GOL D1276
7
AC7
SOFTWARE
ARG A:97 , TRP A:147 , VAL A:152 , LEU A:156 , VAL C:3 , MET C:5 , ALA C:7
BINDING SITE FOR RESIDUE GOL A1276
8
AC8
SOFTWARE
TYR D:84 , TYR D:85 , ASN D:86 , ALA D:139
BINDING SITE FOR RESIDUE GOL D1277
9
AC9
SOFTWARE
PHE A:8 , MET A:98 , SER B:57 , LYS B:58 , HOH B:2069
BINDING SITE FOR RESIDUE GOL B1100
[
close Site info
]
SAPs(SNPs)/Variants
(22, 44)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004334 (F9Y, chain A/D, )
02: VAR_004335 (D30N, chain A/D, )
03: VAR_016726 (A41G, chain A/D, )
04: VAR_004336 (Q43R, chain A/D, )
05: VAR_004337 (K66N, chain A/D, )
06: VAR_016727 (H70Q, chain A/D, )
07: VAR_004338 (T73I, chain A/D, )
08: VAR_016728 (H74D, chain A/D, )
09: VAR_004339 (V95L, chain A/D, )
10: VAR_004340 (R97M, chain A/D, )
11: VAR_004341 (Y99C, chain A/D, )
12: VAR_004342 (Y99F, chain A/D, )
13: VAR_004343 (W107G, chain A/D, )
14: VAR_004344 (M138K, chain A/D, )
15: VAR_004345 (A149T, chain A/D, )
16: VAR_004346 (V152E, chain A/D, )
17: VAR_004348 (L156Q, chain A/D, )
18: VAR_004347 (L156W, chain A/D, )
19: VAR_004349 (T163E, chain A/D, )
20: VAR_016729 (E166D, chain A/D, )
21: VAR_016730 (W167G, chain A/D, )
22: VAR_004350 (A236E, chain A/D, )
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/D
F
9
Y
02
UniProt
VAR_004335
D
54
N
1A02_HUMAN
Polymorphism
---
A/D
D
30
N
03
UniProt
VAR_016726
A
65
G
1A02_HUMAN
Polymorphism
---
A/D
A
41
G
04
UniProt
VAR_004336
Q
67
R
1A02_HUMAN
Polymorphism
---
A/D
Q
43
R
05
UniProt
VAR_004337
K
90
N
1A02_HUMAN
Polymorphism
---
A/D
K
66
N
06
UniProt
VAR_016727
H
94
Q
1A02_HUMAN
Polymorphism
---
A/D
H
70
Q
07
UniProt
VAR_004338
T
97
I
1A02_HUMAN
Polymorphism
---
A/D
T
73
I
08
UniProt
VAR_016728
H
98
D
1A02_HUMAN
Polymorphism
---
A/D
H
74
D
09
UniProt
VAR_004339
V
119
L
1A02_HUMAN
Polymorphism
---
A/D
V
95
L
10
UniProt
VAR_004340
R
121
M
1A02_HUMAN
Polymorphism
---
A/D
R
97
M
11
UniProt
VAR_004341
Y
123
C
1A02_HUMAN
Polymorphism
---
A/D
Y
99
C
12
UniProt
VAR_004342
Y
123
F
1A02_HUMAN
Polymorphism
---
A/D
Y
99
F
13
UniProt
VAR_004343
W
131
G
1A02_HUMAN
Polymorphism
---
A/D
W
107
G
14
UniProt
VAR_004344
M
162
K
1A02_HUMAN
Polymorphism
---
A/D
M
138
K
15
UniProt
VAR_004345
A
173
T
1A02_HUMAN
Polymorphism
---
A/D
A
149
T
16
UniProt
VAR_004346
V
176
E
1A02_HUMAN
Polymorphism
---
A/D
V
152
E
17
UniProt
VAR_004348
L
180
Q
1A02_HUMAN
Polymorphism
---
A/D
L
156
Q
18
UniProt
VAR_004347
L
180
W
1A02_HUMAN
Polymorphism
---
A/D
L
156
W
19
UniProt
VAR_004349
T
187
E
1A02_HUMAN
Polymorphism
---
A/D
T
163
E
20
UniProt
VAR_016729
E
190
D
1A02_HUMAN
Polymorphism
---
A/D
E
166
D
21
UniProt
VAR_016730
W
191
G
1A02_HUMAN
Polymorphism
---
A/D
W
167
G
22
UniProt
VAR_004350
A
260
E
1A02_HUMAN
Polymorphism
---
A/D
A
236
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84,E:78-84,A:257-263,D:257-26...)
;
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
2
B:78-84
E:78-84
1A02_HUMAN
281-287
2
A:257-263
D:257-263
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2x4rb_ (B:)
1b: SCOP_d2x4re_ (E:)
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
d2x4rb_
B:
1b
d2x4re_
E:
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2x4rA01 (A:1-181)
1b: CATH_2x4rD01 (D:1-181)
2a: CATH_2x4rB00 (B:0-99)
2b: CATH_2x4rA02 (A:182-270)
2c: CATH_2x4rD02 (D:182-270)
2d: CATH_2x4rE00 (E:0-99)
View:
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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
2x4rA01
A:1-181
1b
2x4rD01
D:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2x4rB00
B:0-99
2b
2x4rA02
A:182-270
2c
2x4rD02
D:182-270
2d
2x4rE00
E:0-99
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_C1_set_2x4rD01 (D:188-271)
1b: PFAM_C1_set_2x4rD02 (D:188-271)
1c: PFAM_C1_set_2x4rE01 (E:11-92)
1d: PFAM_C1_set_2x4rE02 (E:11-92)
2a: PFAM_MHC_I_2x4rD03 (D:1-179)
2b: PFAM_MHC_I_2x4rD04 (D:1-179)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-2x4rD01
D:188-271
1b
C1-set-2x4rD02
D:188-271
1c
C1-set-2x4rE01
E:11-92
1d
C1-set-2x4rE02
E:11-92
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
2a
MHC_I-2x4rD03
D:1-179
2b
MHC_I-2x4rD04
D:1-179
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select residue range 5 to 10 in all chains
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Asym.Unit (287 KB)
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