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1H15
Asym. Unit
Info
Asym.Unit (139 KB)
Biol.Unit 1 (68 KB)
Biol.Unit 2 (68 KB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF HLA-DRA1*0101/DRB5*0101 COMPLEXED WITH A PEPTIDE FROM EPSTEIN BARR VIRUS DNA POLYMERASE
Authors
:
H. Lang, H. Jacobsen, S. Ikemizu, C. Andersson, K. Harlos, L. Madsen, P. Hjorth, L. Sondergaard, A. Svejgaard, K. Wucherpfennig, D. I. Stuart, J. I. Bell, E. Y. Jones, L. Fugger
Date
:
02 Jul 02 (Deposition) - 03 Oct 02 (Release) - 27 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Immune System/Transferase, Complex (Mhc/Antigen), Immune System, Mhc, Hla, Class Ii, Dr2, Drb5, Ebv, Peptide, Dna Polymerase, Dna-Directed Dna Polymerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Lang, H. Jacobsen, S. Ikemizu, C. Andersson, K. Harlos, L. Madsen, P. Hjorth, L. Sondergaard, A. Svejgaard, K. Wucherpfennig, D. I. Stuart, J. I. Bell, E. Y. Jones, L. Fugger
A Functional And Structural Basis For Tcr Cross-Reactivity In Multiple Sclerosis
Nat. Immunol. V. 3 940 2002
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Hetero Components
(1, 5)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:78
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 78 RESIDUES 1185 TO 1185
2
AC2
SOFTWARE
ASN A:118 , GLU A:166 , TRP A:168 , ASP B:2
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 118 RESIDUES 1183 TO 1184
3
AC3
SOFTWARE
ASN D:78
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 78 RESIDUES 1184 TO 1184
4
AC4
SOFTWARE
VAL D:117 , ASN D:118 , GLU D:166
BINDING SITE FOR MONO-SACCHARIDE NAG D1183 BOUND TO ASN D 118
[
close Site info
]
SAPs(SNPs)/Variants
(32, 64)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_050356 (R4Q, chain B/E, )
02: VAR_060954 (R6C, chain B/E, )
03: VAR_050357 (K12T, chain B/E, )
04: VAR_060955 (H28Q, chain B/E, )
05: VAR_060956 (D30G, chain B/E, )
06: VAR_060957 (D30H, chain B/E, )
07: VAR_050358 (N33H, chain B/E, )
08: VAR_060958 (D37N, chain B/E, )
09: VAR_060959 (D37Y, chain B/E, )
10: VAR_060960 (L38V, chain B/E, )
11: VAR_060961 (A58E, chain B/E, )
12: VAR_060962 (Y60S, chain B/E, )
13: VAR_060964 (F67I, chain B/E, )
14: VAR_060963 (F67L, chain B/E, )
15: VAR_060965 (D70E, chain B/E, )
16: VAR_060966 (D70G, chain B/E, )
17: VAR_060967 (D70H, chain B/E, )
18: VAR_060968 (D70N, chain B/E, )
19: VAR_060969 (D70Q, chain B/E, )
20: VAR_060970 (D70R, chain B/E, )
21: VAR_060971 (R71A, chain B/E, )
22: VAR_060972 (R71G, chain B/E, )
23: VAR_060973 (R71T, chain B/E, )
24: VAR_060974 (A74E, chain B/E, )
25: VAR_060975 (A74L, chain B/E, )
26: VAR_050359 (T77N, chain B/E, )
27: VAR_060976 (Y78V, chain B/E, )
28: VAR_060977 (V85A, chain B/E, )
29: VAR_060978 (G86V, chain B/E, )
30: VAR_039872 (G125A, chain B/E, )
31: VAR_060979 (S135G, chain B/E, )
32: VAR_060980 (T157I, chain B/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_050356
R
33
Q
DRB5_HUMAN
Polymorphism
34716432
B/E
R
4
Q
02
UniProt
VAR_060954
R
35
C
DRB5_HUMAN
Polymorphism
41560013
B/E
R
6
C
03
UniProt
VAR_050357
K
41
T
DRB5_HUMAN
Polymorphism
1136756
B/E
K
12
T
04
UniProt
VAR_060955
H
57
Q
DRB5_HUMAN
Polymorphism
1059345
B/E
H
28
Q
05
UniProt
VAR_060956
D
59
G
DRB5_HUMAN
Polymorphism
41546317
B/E
D
30
G
06
UniProt
VAR_060957
D
59
H
DRB5_HUMAN
Polymorphism
707955
B/E
D
30
H
07
UniProt
VAR_050358
N
62
H
DRB5_HUMAN
Polymorphism
1059576
B/E
N
33
H
08
UniProt
VAR_060958
D
66
N
DRB5_HUMAN
Polymorphism
707956
B/E
D
37
N
09
UniProt
VAR_060959
D
66
Y
DRB5_HUMAN
Polymorphism
77853982
B/E
D
37
Y
10
UniProt
VAR_060960
L
67
V
DRB5_HUMAN
Polymorphism
1059580
B/E
L
38
V
11
UniProt
VAR_060961
A
87
E
DRB5_HUMAN
Polymorphism
---
B/E
A
58
E
12
UniProt
VAR_060962
Y
89
S
DRB5_HUMAN
Polymorphism
41541218
B/E
Y
60
S
13
UniProt
VAR_060964
F
96
I
DRB5_HUMAN
Polymorphism
41562819
B/E
F
67
I
14
UniProt
VAR_060963
F
96
L
DRB5_HUMAN
Polymorphism
41562819
B/E
F
67
L
15
UniProt
VAR_060965
D
99
E
DRB5_HUMAN
Polymorphism
41559913
B/E
D
70
E
16
UniProt
VAR_060966
D
99
G
DRB5_HUMAN
Polymorphism
41545413
B/E
D
70
G
17
UniProt
VAR_060967
D
99
H
DRB5_HUMAN
Polymorphism
41547217
B/E
D
70
H
18
UniProt
VAR_060968
D
99
N
DRB5_HUMAN
Polymorphism
---
B/E
D
70
N
19
UniProt
VAR_060969
D
99
Q
DRB5_HUMAN
Polymorphism
---
B/E
D
70
Q
20
UniProt
VAR_060970
D
99
R
DRB5_HUMAN
Polymorphism
---
B/E
D
70
R
21
UniProt
VAR_060971
R
100
A
DRB5_HUMAN
Polymorphism
---
B/E
R
71
A
22
UniProt
VAR_060972
R
100
G
DRB5_HUMAN
Polymorphism
41551116
B/E
R
71
G
23
UniProt
VAR_060973
R
100
T
DRB5_HUMAN
Polymorphism
41544215
B/E
R
71
T
24
UniProt
VAR_060974
A
103
E
DRB5_HUMAN
Polymorphism
1059598
B/E
A
74
E
25
UniProt
VAR_060975
A
103
L
DRB5_HUMAN
Polymorphism
---
B/E
A
74
L
26
UniProt
VAR_050359
T
106
N
DRB5_HUMAN
Polymorphism
16822752
B/E
T
77
N
27
UniProt
VAR_060976
Y
107
V
DRB5_HUMAN
Polymorphism
---
B/E
Y
78
V
28
UniProt
VAR_060977
V
114
A
DRB5_HUMAN
Polymorphism
1136778
B/E
V
85
A
29
UniProt
VAR_060978
G
115
V
DRB5_HUMAN
Polymorphism
---
B/E
G
86
V
30
UniProt
VAR_039872
G
154
A
DRB5_HUMAN
Polymorphism
---
B/E
G
125
A
31
UniProt
VAR_060979
S
164
G
DRB5_HUMAN
Polymorphism
---
B/E
S
135
G
32
UniProt
VAR_060980
T
186
I
DRB5_HUMAN
Polymorphism
41559420
B/E
T
157
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:161-167,D:161-167,B:171-177,E:17...)
;
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.
DRA_HUMAN
186-192
2
A:161-167
D:161-167
DRB5_HUMAN
200-206
2
B:171-177
E:171-177
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.1 (B:2-5 | E:2-5)
Exon 1.2 (B:5-95 | E:5-95)
Exon 1.3 (B:95-189 | E:95-189)
Exon 1.4 (B:189-190 | E:189-190)
Exon 2.6a (A:3-3 | D:3-3)
Exon 2.7b (A:3-85 | D:3-85)
Exon 2.8c (A:85-179 | D:85-179)
Exon 2.9a (A:179-182 | D:179-182)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary -/2.6a
07: Boundary 2.6a/2.7b
08: Boundary 2.7b/2.8c
09: Boundary 2.8c/2.9a
10: Boundary 2.9a/2.10b
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
ENST00000374975
1
ENSE00001920389
chr6:
32498064-32497902
163
DRB5_HUMAN
1-34
34
2
B:2-5
E:2-5
4
4
1.2
ENST00000374975
2
ENSE00001768120
chr6:
32489951-32489682
270
DRB5_HUMAN
34-124
91
2
B:5-95
E:5-95
91
91
1.3
ENST00000374975
3
ENSE00001641881
chr6:
32487428-32487147
282
DRB5_HUMAN
124-218
95
2
B:95-189
E:95-189
95
95
1.4
ENST00000374975
4
ENSE00001715371
chr6:
32486443-32486333
111
DRB5_HUMAN
218-255
38
2
B:189-190
E:189-190
2
2
1.5
ENST00000374975
5
ENSE00001776788
chr6:
32485854-32485831
24
DRB5_HUMAN
255-263
9
0
-
-
1.6
ENST00000374975
6
ENSE00001833430
chr6:
32485529-32485120
410
DRB5_HUMAN
263-266
4
0
-
-
2.6a
ENST00000383259
6a
ENSE00001839042
HSCHR6_MHC_QBL:32365090-32365280
191
DRA_HUMAN
1-28
28
2
A:3-3
D:3-3
1
1
2.7b
ENST00000383259
7b
ENSE00001719010
HSCHR6_MHC_QBL:32367694-32367939
246
DRA_HUMAN
28-110
83
2
A:3-85
D:3-85
83
83
2.8c
ENST00000383259
8c
ENSE00001737588
HSCHR6_MHC_QBL:32368431-32368712
282
DRA_HUMAN
110-204
95
2
A:85-179
D:85-179
95
95
2.9a
ENST00000383259
9a
ENSE00001770912
HSCHR6_MHC_QBL:32369002-32369167
166
DRA_HUMAN
204-254
51
2
A:179-182
D:179-182
4
4
2.10b
ENST00000383259
10b
ENSE00001925700
HSCHR6_MHC_QBL:32369906-32370300
395
DRA_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1h15a1 (A:82-182)
1b: SCOP_d1h15d1 (D:82-182)
2a: SCOP_d1h15b1 (B:93-190)
2b: SCOP_d1h15e1 (E:93-190)
3a: SCOP_d1h15a2 (A:3-81)
3b: SCOP_d1h15d2 (D:3-81)
4a: SCOP_d1h15b2 (B:2-92)
4b: SCOP_d1h15e2 (E:2-92)
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Classes
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)
(
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Folds
(
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(
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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
:
Class II MHC alpha chain, C-terminal domain
(75)
Human (Homo sapiens), HLA-DR group [TaxId: 9606]
(37)
1a
d1h15a1
A:82-182
1b
d1h15d1
D:82-182
Protein domain
:
Class II MHC beta chain, C-terminal domain
(70)
Human (Homo sapiens), HLA-DR group [TaxId: 9606]
(40)
2a
d1h15b1
B:93-190
2b
d1h15e1
E:93-190
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 II MHC alpha chain, N-terminal domain
(75)
Human (Homo sapiens), HLA-DR1 [TaxId: 9606]
(18)
3a
d1h15a2
A:3-81
3b
d1h15d2
D:3-81
Protein domain
:
Class II MHC beta chain, N-terminal domain
(70)
Human (Homo sapiens), HLA-DR1 [TaxId: 9606]
(17)
4a
d1h15b2
B:2-92
4b
d1h15e2
E:2-92
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1h15B01 (B:2-92)
1b: CATH_1h15A01 (A:3-81)
1c: CATH_1h15D01 (D:3-81)
1d: CATH_1h15E01 (E:2-92)
2a: CATH_1h15A02 (A:82-181)
2b: CATH_1h15D02 (D:82-181)
2c: CATH_1h15B02 (B:93-190)
2d: CATH_1h15E02 (E:93-190)
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Topologies
(
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(
)
Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
(75)
Homologous Superfamily
:
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
(75)
Human (Homo sapiens)
(48)
1a
1h15B01
B:2-92
1b
1h15A01
A:3-81
1c
1h15D01
D:3-81
1d
1h15E01
E:2-92
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1h15A02
A:82-181
2b
1h15D02
D:82-181
2c
1h15B02
B:93-190
2d
1h15E02
E:93-190
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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