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2X4N
Biol. Unit 2
Info
Asym.Unit (282 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (139 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MHC CLASS I HLA-A2.1 BOUND TO RESIDUAL FRAGMENTS OF A PHOTOCLEAVABLE PEPTIDE THAT IS CLEAVED UPON UV-LIGHT TREATMENT
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
:
2.34
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Glycoprotein, Immune System, Transmembrane, Disease Mutation, Immunoglobulin Domain, Phosphoprotein, Immune Response, Host-Virus Interaction, Pyrrolidone Carboxylic Acid, Glycation, Amyloidosis
(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
]
Hetero Components
(3, 10)
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)
1j: GLYCEROL (GOLj)
2a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
2b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
3a: (2R)-AMINO(2-NITROPHENYL)ETHANOIC ... (PRVa)
3b: (2R)-AMINO(2-NITROPHENYL)ETHANOIC ... (PRVb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
7
Ligand/Ion
GLYCEROL
2
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3
PRV
1
Mod. Amino Acid
(2R)-AMINO(2-NITROPHENYL)ETHANOIC ACID
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC5 (SOFTWARE)
5: AC6 (SOFTWARE)
6: AC7 (SOFTWARE)
7: BC1 (SOFTWARE)
8: BC2 (SOFTWARE)
9: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS D:191 , ARG D:201 , ASP E:96 , ASP E:98 , MET E:99
BINDING SITE FOR RESIDUE MES E1100
2
AC2
SOFTWARE
PRO D:234 , PHE D:240 , GOL D:1277 , HOH D:2069 , TYR E:26
BINDING SITE FOR RESIDUE GOL D1275
3
AC4
SOFTWARE
GLU D:231 , THR D:232 , HOH D:2070
BINDING SITE FOR RESIDUE MES D1276
4
AC5
SOFTWARE
ARG D:233 , GLN D:241 , SER E:11 , PRO E:14 , ARG E:97
BINDING SITE FOR RESIDUE GOL E1101
5
AC6
SOFTWARE
PHE D:7 , MET D:97 , PHE E:56 , SER E:57 , LYS E:58 , HOH E:2037 , HOH E:2038
BINDING SITE FOR RESIDUE GOL E1102
6
AC7
SOFTWARE
ARG D:5 , PHE D:7 , ASP D:28 , ASP D:29 , GOL D:1275 , HOH D:2007 , TYR E:63 , HOH E:2024
BINDING SITE FOR RESIDUE GOL D1277
7
BC1
SOFTWARE
THR D:186 , HIS D:187 , HOH D:2048
BINDING SITE FOR RESIDUE GOL D1278
8
BC2
SOFTWARE
ASP A:61 , ASP D:182 , ASP D:237
BINDING SITE FOR RESIDUE GOL D1279
9
BC3
SOFTWARE
ASP D:226 , GLU D:228 , ALA D:245 , VAL D:247
BINDING SITE FOR RESIDUE GOL D1280
[
close Site info
]
SAPs(SNPs)/Variants
(22, 22)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_004334 (F8Y, chain D/A, )
02: VAR_004335 (D29N, chain D/A, )
03: VAR_016726 (A40G, chain D/A, )
04: VAR_004336 (Q42R, chain D/A, )
05: VAR_004337 (K65N, chain D/A, )
06: VAR_016727 (H69Q, chain D/A, )
07: VAR_004338 (T72I, chain D/A, )
08: VAR_016728 (H73D, chain D/A, )
09: VAR_004339 (V94L, chain D/A, )
10: VAR_004340 (R96M, chain D/A, )
11: VAR_004341 (Y98C, chain D/A, )
12: VAR_004342 (Y98F, chain D/A, )
13: VAR_004343 (W106G, chain D/A, )
14: VAR_004344 (M137K, chain D/A, )
15: VAR_004345 (A148T, chain D/A, )
16: VAR_004346 (V151E, chain D/A, )
17: VAR_004348 (L155Q, chain D/A, )
18: VAR_004347 (L155W, chain D/A, )
19: VAR_004349 (T162E, chain D/A, )
20: VAR_016729 (E165D, chain D/A, )
21: VAR_016730 (W166G, chain D/A, )
22: VAR_004350 (A235E, chain D/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
---
D
A
F
8
9
Y
02
UniProt
VAR_004335
D
54
N
1A02_HUMAN
Polymorphism
---
D
A
D
29
30
N
03
UniProt
VAR_016726
A
65
G
1A02_HUMAN
Polymorphism
---
D
A
A
40
41
G
04
UniProt
VAR_004336
Q
67
R
1A02_HUMAN
Polymorphism
---
D
A
Q
42
43
R
05
UniProt
VAR_004337
K
90
N
1A02_HUMAN
Polymorphism
---
D
A
K
65
66
N
06
UniProt
VAR_016727
H
94
Q
1A02_HUMAN
Polymorphism
---
D
A
H
69
70
Q
07
UniProt
VAR_004338
T
97
I
1A02_HUMAN
Polymorphism
---
D
A
T
72
73
I
08
UniProt
VAR_016728
H
98
D
1A02_HUMAN
Polymorphism
---
D
A
H
73
74
D
09
UniProt
VAR_004339
V
119
L
1A02_HUMAN
Polymorphism
---
D
A
V
94
95
L
10
UniProt
VAR_004340
R
121
M
1A02_HUMAN
Polymorphism
---
D
A
R
96
97
M
11
UniProt
VAR_004341
Y
123
C
1A02_HUMAN
Polymorphism
---
D
A
Y
98
99
C
12
UniProt
VAR_004342
Y
123
F
1A02_HUMAN
Polymorphism
---
D
A
Y
98
99
F
13
UniProt
VAR_004343
W
131
G
1A02_HUMAN
Polymorphism
---
D
A
W
106
107
G
14
UniProt
VAR_004344
M
162
K
1A02_HUMAN
Polymorphism
---
D
A
M
137
138
K
15
UniProt
VAR_004345
A
173
T
1A02_HUMAN
Polymorphism
---
D
A
A
148
149
T
16
UniProt
VAR_004346
V
176
E
1A02_HUMAN
Polymorphism
---
D
A
V
151
152
E
17
UniProt
VAR_004348
L
180
Q
1A02_HUMAN
Polymorphism
---
D
A
L
155
156
Q
18
UniProt
VAR_004347
L
180
W
1A02_HUMAN
Polymorphism
---
D
A
L
155
156
W
19
UniProt
VAR_004349
T
187
E
1A02_HUMAN
Polymorphism
---
D
A
T
162
163
E
20
UniProt
VAR_016729
E
190
D
1A02_HUMAN
Polymorphism
---
D
A
E
165
166
D
21
UniProt
VAR_016730
W
191
G
1A02_HUMAN
Polymorphism
---
D
A
W
166
167
G
22
UniProt
VAR_004350
A
260
E
1A02_HUMAN
Polymorphism
---
D
A
A
235
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 (E:78-84)
;
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
-
E:78-84
1A02_HUMAN
281-287
1
-
D:256-262
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2x4nb_ (B:)
1b: SCOP_d2x4ne_ (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
d2x4nb_
B:
1b
d2x4ne_
E:
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2x4nA01 (A:1-181)
1b: CATH_2x4nD01 (D:0-180)
2a: CATH_2x4nB00 (B:0-99)
2b: CATH_2x4nA02 (A:182-270)
2c: CATH_2x4nD02 (D:181-269)
2d: CATH_2x4nE00 (E:0-99)
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
2x4nA01
A:1-181
1b
2x4nD01
D:0-180
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2x4nB00
B:0-99
2b
2x4nA02
A:182-270
2c
2x4nD02
D:181-269
2d
2x4nE00
E:0-99
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_C1_set_2x4nD01 (D:187-270)
1b: PFAM_C1_set_2x4nD02 (D:187-270)
1c: PFAM_C1_set_2x4nE01 (E:11-92)
1d: PFAM_C1_set_2x4nE02 (E:11-92)
2a: PFAM_MHC_I_2x4nD03 (D:1-178)
2b: PFAM_MHC_I_2x4nD04 (D:1-178)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-2x4nD01
D:187-270
1b
C1-set-2x4nD02
D:187-270
1c
C1-set-2x4nE01
E:11-92
1d
C1-set-2x4nE02
E:11-92
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
2a
MHC_I-2x4nD03
D:1-178
2b
MHC_I-2x4nD04
D:1-178
[
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]
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)
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Nucleic
Backbone
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Solvent
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Protein & NOT Site
Protein & NOT PROSITE
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Chain E
Chain F
Asymmetric Unit 1
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