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2Q6W
Asym. Unit
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Asym.Unit (140 KB)
Biol.Unit 1 (68 KB)
Biol.Unit 2 (69 KB)
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(1)
Title
:
THE STRUCTURE OF HLA-DRA, DRB3*0101 (DR52A) WITH BOUND PLATELET INTEGRIN PEPTIDE ASSOCIATED WITH FETAL AND NEONATAL ALLOIMMUNE THROMBOCYTOPENIA
Authors
:
C. S. Parry
Date
:
05 Jun 07 (Deposition) - 24 Jul 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Drb3, Peptide-Class Ii Mhc Complex, Fetal-Maternal Alloimmune Thrombocytopenia, Thrombocytopenia Purpura, Myasthenia Gravis, Beta 11 Arginine, Autoimmunity, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. S. Parry, J. Gorski, L. J. Stern
Crystallographic Structure Of The Human Leukocyte Antigen Dra, Drb3*0101: Models Of A Directional Alloimmune Response And Autoimmunity
J. Mol. Biol. V. 371 435 2007
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
Info
All Hetero Components
View:
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Label:
Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
View:
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Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(43, 86)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_060739 (L8S, chain B/E, )
02: VAR_060740 (E9Q, chain B/E, )
03: VAR_060741 (L10Y, chain B/E, )
04: VAR_016686 (R11C, chain B/E, )
05: VAR_060742 (R11L, chain B/E, )
06: VAR_060743 (R11S, chain B/E, )
07: VAR_060744 (K12T, chain B/E, )
08: VAR_060746 (Y26F, chain B/E, )
09: VAR_060745 (Y26L, chain B/E, )
10: VAR_060747 (D28E, chain B/E, )
11: VAR_060748 (D28N, chain B/E, )
12: VAR_060749 (R29I, chain B/E, )
13: VAR_060750 (Y30H, chain B/E, )
14: VAR_003993 (L33P, chain C/F, )
15: VAR_060752 (F37L, chain B/E, )
16: VAR_060753 (F37N, chain B/E, )
17: VAR_060751 (F37S, chain B/E, )
18: VAR_060754 (F37Y, chain B/E, )
19: VAR_060755 (L38A, chain B/E, )
20: VAR_060756 (L38V, chain B/E, )
21: VAR_060757 (R39S, chain B/E, )
22: VAR_060758 (T51R, chain B/E, )
23: VAR_060759 (R55L, chain B/E, )
24: VAR_060760 (V57A, chain B/E, )
25: VAR_060762 (V57D, chain B/E, )
26: VAR_060761 (V57S, chain B/E, )
27: VAR_060763 (A58E, chain B/E, )
28: VAR_060764 (S60H, chain B/E, )
29: VAR_060765 (S60Y, chain B/E, )
30: VAR_060766 (L67F, chain B/E, )
31: VAR_060767 (L67I, chain B/E, )
32: VAR_033396 (G73A, chain B/E, )
33: VAR_060768 (R74Q, chain B/E, )
34: VAR_060769 (N77T, chain B/E, )
35: VAR_060770 (G84R, chain B/E, )
36: VAR_033397 (V85A, chain B/E, )
37: VAR_060771 (G86A, chain B/E, )
38: VAR_060772 (G86V, chain B/E, )
39: VAR_060773 (A140T, chain B/E, )
40: VAR_060774 (Q149H, chain B/E, )
41: VAR_060775 (V164F, chain B/E, )
42: VAR_060776 (A183P, chain B/E, )
43: VAR_060777 (R189S, chain B/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_060739
L
37
S
DRB3_HUMAN
Polymorphism
---
B/E
L
8
S
02
UniProt
VAR_060740
E
38
Q
DRB3_HUMAN
Polymorphism
---
B/E
E
9
Q
03
UniProt
VAR_060741
L
39
Y
DRB3_HUMAN
Polymorphism
---
B/E
L
10
Y
04
UniProt
VAR_016686
R
40
C
DRB3_HUMAN
Polymorphism
---
B/E
R
11
C
05
UniProt
VAR_060742
R
40
L
DRB3_HUMAN
Polymorphism
---
B/E
R
11
L
06
UniProt
VAR_060743
R
40
S
DRB3_HUMAN
Polymorphism
---
B/E
R
11
S
07
UniProt
VAR_060744
K
41
T
DRB3_HUMAN
Polymorphism
---
B/E
K
12
T
08
UniProt
VAR_060746
Y
55
F
DRB3_HUMAN
Polymorphism
---
B/E
Y
26
F
09
UniProt
VAR_060745
Y
55
L
DRB3_HUMAN
Polymorphism
---
B/E
Y
26
L
10
UniProt
VAR_060747
D
57
E
DRB3_HUMAN
Polymorphism
---
B/E
D
28
E
11
UniProt
VAR_060748
D
57
N
DRB3_HUMAN
Polymorphism
---
B/E
D
28
N
12
UniProt
VAR_060749
R
58
I
DRB3_HUMAN
Polymorphism
---
B/E
R
29
I
13
UniProt
VAR_060750
Y
59
H
DRB3_HUMAN
Polymorphism
---
B/E
Y
30
H
14
UniProt
VAR_003993
L
59
P
ITB3_HUMAN
Polymorphism
5918
C/F
L
33
P
15
UniProt
VAR_060752
F
66
L
DRB3_HUMAN
Polymorphism
---
B/E
F
37
L
16
UniProt
VAR_060753
F
66
N
DRB3_HUMAN
Polymorphism
---
B/E
F
37
N
17
UniProt
VAR_060751
F
66
S
DRB3_HUMAN
Polymorphism
---
B/E
F
37
S
18
UniProt
VAR_060754
F
66
Y
DRB3_HUMAN
Polymorphism
---
B/E
F
37
Y
19
UniProt
VAR_060755
L
67
A
DRB3_HUMAN
Polymorphism
---
B/E
L
38
A
20
UniProt
VAR_060756
L
67
V
DRB3_HUMAN
Polymorphism
---
B/E
L
38
V
21
UniProt
VAR_060757
R
68
S
DRB3_HUMAN
Polymorphism
---
B/E
R
39
S
22
UniProt
VAR_060758
T
80
R
DRB3_HUMAN
Polymorphism
---
B/E
T
51
R
23
UniProt
VAR_060759
R
84
L
DRB3_HUMAN
Polymorphism
---
B/E
R
55
L
24
UniProt
VAR_060760
V
86
A
DRB3_HUMAN
Polymorphism
---
B/E
V
57
A
25
UniProt
VAR_060762
V
86
D
DRB3_HUMAN
Polymorphism
---
B/E
V
57
D
26
UniProt
VAR_060761
V
86
S
DRB3_HUMAN
Polymorphism
---
B/E
V
57
S
27
UniProt
VAR_060763
A
87
E
DRB3_HUMAN
Polymorphism
---
B/E
A
58
E
28
UniProt
VAR_060764
S
89
H
DRB3_HUMAN
Polymorphism
---
B/E
S
60
H
29
UniProt
VAR_060765
S
89
Y
DRB3_HUMAN
Polymorphism
---
B/E
S
60
Y
30
UniProt
VAR_060766
L
96
F
DRB3_HUMAN
Polymorphism
---
B/E
L
67
F
31
UniProt
VAR_060767
L
96
I
DRB3_HUMAN
Polymorphism
---
B/E
L
67
I
32
UniProt
VAR_033396
G
102
A
DRB3_HUMAN
Polymorphism
17878857
B/E
G
73
A
33
UniProt
VAR_060768
R
103
Q
DRB3_HUMAN
Polymorphism
---
B/E
R
74
Q
34
UniProt
VAR_060769
N
106
T
DRB3_HUMAN
Polymorphism
---
B/E
N
77
T
35
UniProt
VAR_060770
G
113
R
DRB3_HUMAN
Polymorphism
---
B/E
G
84
R
36
UniProt
VAR_033397
V
114
A
DRB3_HUMAN
Polymorphism
17424145
B/E
V
85
A
37
UniProt
VAR_060771
G
115
A
DRB3_HUMAN
Polymorphism
---
B/E
G
86
A
38
UniProt
VAR_060772
G
115
V
DRB3_HUMAN
Polymorphism
---
B/E
G
86
V
39
UniProt
VAR_060773
A
169
T
DRB3_HUMAN
Polymorphism
---
B/E
A
140
T
40
UniProt
VAR_060774
Q
178
H
DRB3_HUMAN
Polymorphism
---
B/E
Q
149
H
41
UniProt
VAR_060775
V
193
F
DRB3_HUMAN
Polymorphism
---
B/E
V
164
F
42
UniProt
VAR_060776
A
212
P
DRB3_HUMAN
Polymorphism
---
B/E
A
183
P
43
UniProt
VAR_060777
R
218
S
DRB3_HUMAN
Polymorphism
---
B/E
R
189
S
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
DRB3_HUMAN
200-206
2
B:171-177
E:171-177
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.2 (B:3-5 | E:3-5)
Exon 1.8 (B:5-95 | E:5-95)
Exon 1.9 (B:95-189 | E:95-189)
Exon 1.10 (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 -/1.2
02: Boundary 1.2/1.8
03: Boundary 1.8/1.9
04: Boundary 1.9/1.10
05: Boundary 1.10/1.11
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
1.2
ENST00000383126
2
ENSE00001866449
HSCHR6_MHC_COX:32425028-32424852
177
DRB3_HUMAN
1-34
34
2
B:3-5
E:3-5
3
3
1.8
ENST00000383126
8
ENSE00001683814
HSCHR6_MHC_COX:32417170-32416901
270
DRB3_HUMAN
34-124
91
2
B:5-95
E:5-95
91
91
1.9
ENST00000383126
9
ENSE00001797407
HSCHR6_MHC_COX:32414626-32414345
282
DRB3_HUMAN
124-218
95
2
B:95-189
E:95-189
95
95
1.10
ENST00000383126
10
ENSE00001738307
HSCHR6_MHC_COX:32413660-32413550
111
DRB3_HUMAN
218-255
38
2
B:189-190
E:189-190
2
2
1.11
ENST00000383126
11
ENSE00001615870
HSCHR6_MHC_COX:32413076-32413053
24
DRB3_HUMAN
255-263
9
0
-
-
1.12
ENST00000383126
12
ENSE00001409006
HSCHR6_MHC_COX:32412253-32411911
343
DRB3_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
-
-
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2q6wB01 (B:3-93)
1b: CATH_2q6wE01 (E:3-93)
1c: CATH_2q6wA01 (A:3-81)
1d: CATH_2q6wD01 (D:3-81)
2a: CATH_2q6wA02 (A:82-182)
2b: CATH_2q6wD02 (D:82-182)
2c: CATH_2q6wB02 (B:94-190)
2d: CATH_2q6wE02 (E:94-190)
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
2q6wB01
B:3-93
1b
2q6wE01
E:3-93
1c
2q6wA01
A:3-81
1d
2q6wD01
D:3-81
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2q6wA02
A:82-182
2b
2q6wD02
D:82-182
2c
2q6wB02
B:94-190
2d
2q6wE02
E:94-190
[
close CATH info
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Pfam Domains
(4, 10)
Info
all PFAM domains
1a: PFAM_C1_set_2q6wD01 (D:93-175)
1b: PFAM_C1_set_2q6wD02 (D:93-175)
1c: PFAM_C1_set_2q6wE01 (E:103-190)
1d: PFAM_C1_set_2q6wE02 (E:103-190)
2a: PFAM_MHC_II_alpha_2q6wD03 (D:4-84)
2b: PFAM_MHC_II_alpha_2q6wD04 (D:4-84)
3a: PFAM_MHC_II_beta_2q6wE03 (E:13-87)
3b: PFAM_MHC_II_beta_2q6wE04 (E:13-87)
4a: PFAM_Integrin_beta_2q6wF01 (F:24-35)
4b: PFAM_Integrin_beta_2q6wF02 (F:24-35)
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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-2q6wD01
D:93-175
1b
C1-set-2q6wD02
D:93-175
1c
C1-set-2q6wE01
E:103-190
1d
C1-set-2q6wE02
E:103-190
Clan
:
MHC
(252)
Family
:
MHC_II_alpha
(42)
Homo sapiens (Human)
(26)
2a
MHC_II_alpha-2q6wD03
D:4-84
2b
MHC_II_alpha-2q6wD04
D:4-84
Family
:
MHC_II_beta
(39)
Homo sapiens (Human)
(25)
3a
MHC_II_beta-2q6wE03
E:13-87
3b
MHC_II_beta-2q6wE04
E:13-87
Clan
:
no clan defined [family: Integrin_beta]
(18)
Family
:
Integrin_beta
(18)
Homo sapiens (Human)
(18)
4a
Integrin_beta-2q6wF01
F:24-35
4b
Integrin_beta-2q6wF02
F:24-35
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