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2X4U
Asym. Unit
Info
Asym.Unit (294 KB)
Biol.Unit 1 (139 KB)
Biol.Unit 2 (145 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MHC CLASS I HLA-A2.1 BOUND TO HIV-1 PEPTIDE RT468-476
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
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: D,E,F (1x)
Biol. Unit 2: A,B,C (1x)
Keywords
:
Glycoprotein, Immune System, Transmembrane, Phosphoprotein, Immune Response, Secreted, Glycation, Amyloidosis, Immunoglobulin Domain, Host-Virus Interaction, Amyloid, Membrane, Photocleavable Peptide, Pyrrolidone Carboxylic Acid, Envelope Protein, Disease Mutation
(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
(2, 14)
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)
2a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
2b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
2c: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESc)
2d: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESd)
2e: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
9
Ligand/Ion
GLYCEROL
2
MES
5
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
[
close Hetero Component info
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Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:8 , MET A:98 , GLN A:115 , GOL A:1279 , HOH A:2175 , PHE B:56 , SER B:57 , LYS B:58
BINDING SITE FOR RESIDUE GOL A1276
02
AC2
SOFTWARE
HIS D:192 , THR D:200 , ARG D:202 , ASP E:96 , ASP E:98
BINDING SITE FOR RESIDUE MES D1276
03
AC3
SOFTWARE
PHE D:241 , MES D:1277 , HOH D:2096 , HOH D:2101 , SER E:57 , LYS E:58
BINDING SITE FOR RESIDUE MES E1100
04
AC4
SOFTWARE
PHE A:241 , GOL A:1278 , SER B:57 , LYS B:58 , TYR B:63
BINDING SITE FOR RESIDUE MES B1100
05
AC5
SOFTWARE
GLN A:262 , HIS A:263 , GLU A:264 , LEU A:266 , PRO A:269 , HOH A:2134
BINDING SITE FOR RESIDUE MES A1277
06
AC6
SOFTWARE
TRP A:204 , ARG A:234 , GLN A:242 , SER B:11 , HIS B:13 , PRO B:14 , ALA B:15 , ARG B:97 , HOH B:2085
BINDING SITE FOR RESIDUE GOL B1101
07
AC7
SOFTWARE
GLU D:232 , THR D:233 , HOH D:2080 , HOH D:2096 , HOH D:2097 , HOH D:2098 , HOH D:2099 , MES E:1100
BINDING SITE FOR RESIDUE MES D1277
08
AC8
SOFTWARE
TRP D:204 , LEU D:206 , ARG D:234 , GLN D:242 , HOH D:2062 , SER E:11 , HIS E:13 , PRO E:14
BINDING SITE FOR RESIDUE GOL D1278
09
AC9
SOFTWARE
MET D:98 , PHE E:56 , SER E:57 , LYS E:58
BINDING SITE FOR RESIDUE GOL E1101
10
BC1
SOFTWARE
ARG D:6 , PHE D:8 , ASP D:29 , ASP D:30 , HOH D:2100 , HOH D:2101 , TYR E:63
BINDING SITE FOR RESIDUE GOL D1279
11
BC2
SOFTWARE
ARG A:6 , PHE A:8 , ASP A:29 , ASP A:30 , MES B:1100 , HOH B:2057
BINDING SITE FOR RESIDUE GOL A1278
12
BC3
SOFTWARE
ARG A:6 , MET A:98 , GOL A:1276 , HOH A:2175
BINDING SITE FOR RESIDUE GOL A1279
13
BC4
SOFTWARE
ASP D:183 , ASP D:238 , THR D:240
BINDING SITE FOR RESIDUE GOL D1280
14
BC5
SOFTWARE
VAL D:231 , THR E:4 , PRO E:5 , LYS E:6 , ILE E:7 , LEU E:87 , LYS E:91 , HOH E:2052
BINDING SITE FOR RESIDUE GOL E1102
[
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
[
close PROSITE info
]
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_d2x4ub_ (B:)
1b: SCOP_d2x4ue_ (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
d2x4ub_
B:
1b
d2x4ue_
E:
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2x4uA01 (A:1-181)
1b: CATH_2x4uD01 (D:1-181)
2a: CATH_2x4uB00 (B:0-99)
2b: CATH_2x4uA02 (A:182-270)
2c: CATH_2x4uD02 (D:182-270)
2d: CATH_2x4uE00 (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
2x4uA01
A:1-181
1b
2x4uD01
D:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2x4uB00
B:0-99
2b
2x4uA02
A:182-270
2c
2x4uD02
D:182-270
2d
2x4uE00
E:0-99
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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