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1X7Q
Asym. Unit
Info
Asym.Unit (165 KB)
Biol.Unit 1 (160 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HLA-A*1101 WITH SARS NUCLEOCAPSID PEPTIDE
Authors
:
T. Blicher, J. S. Kastrup, S. Buus, M. Gajhede
Date
:
16 Aug 04 (Deposition) - 02 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Peptide-Mhc-Complex, Major Histocompatibility Complex Class I, Mhc-I, Human Leukocyte Antigen, Hla, Immunoglobulin Family, Sars, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Blicher, J. S. Kastrup, S. Buus, M. Gajhede
High-Resolution Structure Of Hla-A*1101 In Complex With Sar Nucleocapsid Peptide.
Acta Crystallogr. , Sect. D V. 61 1031 2005
[
close entry info
]
Hetero Components
(2, 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)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
7
Ligand/Ion
GLYCEROL
2
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:21 , HIS B:51 , HOH B:5052 , HOH B:5075 , HOH B:5166
BINDING SITE FOR RESIDUE SO4 B 4001
02
AC2
SOFTWARE
ARG A:75 , HOH A:5108
BINDING SITE FOR RESIDUE SO4 A 4002
03
AC3
SOFTWARE
GLN A:62 , ARG A:163 , TRP A:167 , HOH A:5295 , HOH A:5384 , LYS C:1
BINDING SITE FOR RESIDUE SO4 A 4003
04
AC4
SOFTWARE
GLU A:19 , HOH A:5057 , HOH A:5080 , HOH A:5113
BINDING SITE FOR RESIDUE GOL A 5001
05
AC5
SOFTWARE
GLN A:226 , ASP A:227 , HOH A:5089
BINDING SITE FOR RESIDUE GOL A 5002
06
AC6
SOFTWARE
PHE A:8 , TYR A:27 , ASP A:29 , ASP A:30 , HOH A:5109 , HOH A:5140 , HOH A:5177 , HOH A:5334 , HOH A:5349 , TYR B:63
BINDING SITE FOR RESIDUE GOL A 5003
07
AC7
SOFTWARE
VAL A:231 , ARG A:234 , GLN B:8 , MET B:99 , HOH B:5014 , HOH B:5036 , HOH B:5146
BINDING SITE FOR RESIDUE GOL B 5004
08
AC8
SOFTWARE
GLU A:232 , THR A:233 , LYS A:243 , HOH A:5173 , HOH A:5187 , HOH A:5216 , HOH A:5356
BINDING SITE FOR RESIDUE GOL A 5005
09
AC9
SOFTWARE
GLU A:148 , HIS A:151 , GLU A:154 , HOH A:5032 , HOH A:5124 , HOH A:5172 , HOH A:5262
BINDING SITE FOR RESIDUE GOL A 5006
10
BC1
SOFTWARE
SER B:20 , HOH B:5112
BINDING SITE FOR RESIDUE GOL B 5007
[
close Site info
]
SAPs(SNPs)/Variants
(14, 14)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004353 (E19K, chain A, )
02: VAR_056254 (R65G, chain A, )
03: VAR_056255 (Q70H, chain A, )
04: VAR_056256 (D77N, chain A, )
05: VAR_056257 (G107W, chain A, )
06: VAR_016731 (F109L, chain A, )
07: VAR_056258 (N127K, chain A, )
08: VAR_056259 (I142T, chain A, )
09: VAR_016732 (K144E, chain A, )
10: VAR_056260 (R145H, chain A, )
11: VAR_016733 (H151R, chain A, )
12: VAR_016734 (A152E, chain A, )
13: VAR_016735 (R163T, chain A, )
14: VAR_056261 (R181H, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_004353
E
43
K
1A11_HUMAN
Polymorphism
---
A
E
19
K
02
UniProt
VAR_056254
R
89
G
1A11_HUMAN
Polymorphism
1059459
A
R
65
G
03
UniProt
VAR_056255
Q
94
H
1A11_HUMAN
Polymorphism
1059463
A
Q
70
H
04
UniProt
VAR_056256
D
101
N
1A11_HUMAN
Polymorphism
1136688
A
D
77
N
05
UniProt
VAR_056257
G
131
W
1A11_HUMAN
Polymorphism
1136702
A
G
107
W
06
UniProt
VAR_016731
F
133
L
1A11_HUMAN
Polymorphism
1059488
A
F
109
L
07
UniProt
VAR_056258
N
151
K
1A11_HUMAN
Polymorphism
1059509
A
N
127
K
08
UniProt
VAR_056259
I
166
T
1A11_HUMAN
Polymorphism
1059516
A
I
142
T
09
UniProt
VAR_016732
K
168
E
1A11_HUMAN
Polymorphism
---
A
K
144
E
10
UniProt
VAR_056260
R
169
H
1A11_HUMAN
Polymorphism
1059520
A
R
145
H
11
UniProt
VAR_016733
H
175
R
1A11_HUMAN
Polymorphism
---
A
H
151
R
12
UniProt
VAR_016734
A
176
E
1A11_HUMAN
Polymorphism
---
A
A
152
E
13
UniProt
VAR_016735
R
187
T
1A11_HUMAN
Polymorphism
---
A
R
163
T
14
UniProt
VAR_056261
R
205
H
1A11_HUMAN
Polymorphism
17185861
A
R
181
H
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
1A11_HUMAN
281-287
1
A:257-263
[
close PROSITE info
]
Exons
(5, 5)
Info
All Exons
Exon 1.3b (A:1-1)
Exon 1.4b (A:1-91)
Exon 1.4e (A:91-183)
Exon 1.5 (A:183-275)
Exon 1.6a (A:275-275)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3b
2: Boundary 1.3b/1.4b
3: Boundary 1.4b/1.4e
4: Boundary 1.4e/1.5
5: Boundary 1.5/1.6a
6: Boundary 1.6a/1.6d
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
1.1
ENST00000396634
1
ENSE00001677386
chr6:
29909037-29909096
60
1A11_HUMAN
-
0
0
-
-
1.2
ENST00000396634
2
ENSE00001617475
chr6:
29909743-29909873
131
1A11_HUMAN
-
0
0
-
-
1.3b
ENST00000396634
3b
ENSE00001633002
chr6:
29910181-29910403
223
1A11_HUMAN
1-25
25
1
A:1-1
1
1.4b
ENST00000396634
4b
ENSE00001709288
chr6:
29910534-29910803
270
1A11_HUMAN
25-115
91
1
A:1-91
91
1.4e
ENST00000396634
4e
ENSE00001681031
chr6:
29911045-29911320
276
1A11_HUMAN
115-207
93
1
A:91-183
93
1.5
ENST00000396634
5
ENSE00001789740
chr6:
29911899-29912174
276
1A11_HUMAN
207-299
93
1
A:183-275
93
1.6a
ENST00000396634
6a
ENSE00001725298
chr6:
29912277-29912393
117
1A11_HUMAN
299-338
40
1
A:275-275
1
1.6d
ENST00000396634
6d
ENSE00001649179
chr6:
29912836-29912868
33
1A11_HUMAN
338-349
12
0
-
-
1.7
ENST00000396634
7
ENSE00001689328
chr6:
29913011-29913058
48
1A11_HUMAN
349-365
17
0
-
-
1.8b
ENST00000396634
8b
ENSE00001732087
chr6:
29913228-29913661
434
1A11_HUMAN
365-365
1
0
-
-
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1x7qb_ (B:)
2a: SCOP_d1x7qa1 (A:182-275)
3a: SCOP_d1x7qa2 (A:1-181)
View:
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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
d1x7qb_
B:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d1x7qa1
A:182-275
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-A11 [TaxId: 9606]
(4)
3a
d1x7qa2
A:1-181
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1x7qA01 (A:1-181)
2a: CATH_1x7qB00 (B:1-99)
2b: CATH_1x7qA02 (A:182-275)
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
1x7qA01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1x7qB00
B:1-99
2b
1x7qA02
A:182-275
[
close CATH info
]
Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_C1_set_1x7qA01 (A:185-271)
1b: PFAM_C1_set_1x7qB01 (B:11-92)
2a: PFAM_MHC_I_1x7qA02 (A:1-179)
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Clans
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(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-1x7qA01
A:185-271
1b
C1-set-1x7qB01
B:11-92
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
2a
MHC_I-1x7qA02
A:1-179
[
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]
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Nucleic
Backbone
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Protein & NOT Site
Protein & NOT PROSITE
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