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Getting 'Exon' information from database.
1YMM
Asym. Unit
Info
Asym.Unit (129 KB)
Biol.Unit 1 (119 KB)
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(1)
Title
:
TCR/HLA-DR2B/MBP-PEPTIDE COMPLEX
Authors
:
M. Hahn, M. J. Nicholson, J. Pyrdol, K. W. Wucherpfennig
Date
:
21 Jan 05 (Deposition) - 03 May 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Protein-Protein Complex, T Cell Repertoire, Auto-Immunity, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Hahn, M. J. Nicholson, J. Pyrdol, K. W. Wucherpfennig
Unconventional Topology Of Self Peptide-Major Histocompatibility Complex Binding By A Human Autoimmune T Cell Receptor.
Nat. Immunol. V. 6 490 2005
[
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:118 , TRP A:168
BINDING SITE FOR RESIDUE NAG A 192
[
close Site info
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SAPs(SNPs)/Variants
(7, 7)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_050365 (F26Y, chain B, )
2: VAR_038162 (Y30H, chain B, )
3: VAR_038163 (I67F, chain B, )
4: VAR_050366 (T77N, chain B, )
5: VAR_038164 (V86G, chain B, )
6: VAR_050367 (G135S, chain B, )
7: VAR_050368 (A140T, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_050365
F
55
Y
2B1F_HUMAN
Polymorphism
16822516
B
F
26
Y
2
UniProt
VAR_038162
Y
59
H
2B1F_HUMAN
Polymorphism
---
B
Y
30
H
3
UniProt
VAR_038163
I
96
F
2B1F_HUMAN
Polymorphism
17886918
B
I
67
F
4
UniProt
VAR_050366
T
106
N
2B1F_HUMAN
Polymorphism
9269941
B
T
77
N
5
UniProt
VAR_038164
V
115
G
2B1F_HUMAN
Polymorphism
17885482
B
V
86
G
6
UniProt
VAR_050367
G
164
S
2B1F_HUMAN
Polymorphism
1059633
B
G
135
S
7
UniProt
VAR_050368
A
169
T
2B1F_HUMAN
Polymorphism
2308768
B
A
140
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:161-167,B:171-177)
2: MYELIN_MBP (C:88-94)
;
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
1
A:161-167
2B1F_HUMAN
200-206
1
B:171-177
2
MYELIN_MBP
PS00569
Myelin basic protein signature.
MBP_HUMAN
220-226
1
C:88-94
[
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]
Exons
(10, 10)
Info
All Exons
Exon 1.13c (C:85-95)
Exon 1.14e (C:96-98)
Exon 2.3 (B:3-5)
Exon 2.4 (B:5-95)
Exon 2.5b (B:95-189 (gaps))
Exon 2.6 (B:189-189)
Exon 3.6a (A:2-3)
Exon 3.7b (A:3-85)
Exon 3.8c (A:85-179)
Exon 3.9a (A:179-183)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.10e/1.13c
02: Boundary 1.13c/1.14e
03: Boundary 1.14e/1.14g
04: Boundary -/2.3
05: Boundary 2.3/2.4
06: Boundary 2.4/2.5b
07: Boundary 2.5b/2.6
08: Boundary 2.6/2.7
09: Boundary -/3.6a
10: Boundary 3.6a/3.7b
11: Boundary 3.7b/3.8c
12: Boundary 3.8c/3.9a
13: Boundary 3.9a/3.10b
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
1.2a
ENST00000355994
2a
ENSE00001421865
chr18:
74844774-74844536
239
MBP_HUMAN
-
0
0
-
-
1.4
ENST00000355994
4
ENSE00002187900
chr18:
74817242-74817167
76
MBP_HUMAN
1-17
17
0
-
-
1.8a
ENST00000355994
8a
ENSE00001400728
chr18:
74778341-74778254
88
MBP_HUMAN
18-47
30
0
-
-
1.10e
ENST00000355994
10e
ENSE00001432843
chr18:
74729224-74728788
437
MBP_HUMAN
47-192
146
0
-
-
1.13c
ENST00000355994
13c
ENSE00001179369
chr18:
74702016-74701912
105
MBP_HUMAN
193-227
35
1
C:85-95
11
1.14e
ENST00000355994
14e
ENSE00001000086
chr18:
74700868-74700833
36
MBP_HUMAN
228-239
12
1
C:96-98
3
1.14g
ENST00000355994
14g
ENSE00001278460
chr18:
74700483-74700451
33
MBP_HUMAN
240-250
11
0
-
-
1.14o
ENST00000355994
14o
ENSE00001656901
chr18:
74696850-74696731
120
MBP_HUMAN
251-290
40
0
-
-
1.15l
ENST00000355994
15l
ENSE00001606913
chr18:
74692427-74690790
1638
MBP_HUMAN
291-304
14
0
-
-
2.3
ENST00000360004
3
ENSE00001930619
chr6:
32557625-32557420
206
2B1F_HUMAN
1-34
34
1
B:3-5
3
2.4
ENST00000360004
4
ENSE00001731226
chr6:
32552155-32551886
270
2B1F_HUMAN
34-124
91
1
B:5-95
91
2.5b
ENST00000360004
5b
ENSE00001801024
chr6:
32549615-32549334
282
2B1F_HUMAN
124-218
95
1
B:95-189 (gaps)
95
2.6
ENST00000360004
6
ENSE00001717727
chr6:
32548633-32548523
111
2B1F_HUMAN
218-255
38
1
B:189-189
1
2.7
ENST00000360004
7
ENSE00001773376
chr6:
32548047-32548024
24
2B1F_HUMAN
255-263
9
0
-
-
2.8
ENST00000360004
8
ENSE00001954617
chr6:
32546881-32546546
336
2B1F_HUMAN
263-266
4
0
-
-
3.6a
ENST00000383259
6a
ENSE00001839042
HSCHR6_MHC_QBL:32365090-32365280
191
DRA_HUMAN
1-28
28
1
A:2-3
2
3.7b
ENST00000383259
7b
ENSE00001719010
HSCHR6_MHC_QBL:32367694-32367939
246
DRA_HUMAN
28-110
83
1
A:3-85
83
3.8c
ENST00000383259
8c
ENSE00001737588
HSCHR6_MHC_QBL:32368431-32368712
282
DRA_HUMAN
110-204
95
1
A:85-179
95
3.9a
ENST00000383259
9a
ENSE00001770912
HSCHR6_MHC_QBL:32369002-32369167
166
DRA_HUMAN
204-254
51
1
A:179-183
5
3.10b
ENST00000383259
10b
ENSE00001925700
HSCHR6_MHC_QBL:32369906-32370300
395
DRA_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(7, 7)
Info
All SCOP Domains
1a: SCOP_d1ymma1 (A:83-179)
2a: SCOP_d1ymmb1 (B:93-189)
3a: SCOP_d1ymme2 (E:123-246)
4a: SCOP_d1ymmd1 (D:9-104)
5a: SCOP_d1ymme1 (E:1-119)
6a: SCOP_d1ymma2 (A:13-81)
7a: SCOP_d1ymmb2 (B:3-92)
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)
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(
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)
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(
)
(
)
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(
)
(
)
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)
Mouse (Mus musculus), I-A group [TaxId: 10090]
(24)
1a
d1ymma1
A:83-179
Protein domain
:
Class II MHC beta chain, C-terminal domain
(70)
Human (Homo sapiens), HLA-DR group [TaxId: 9606]
(40)
2a
d1ymmb1
B:93-189
Protein domain
:
T-cell antigen receptor
(81)
Human (Homo sapiens), beta-chain [TaxId: 9606]
(29)
3a
d1ymme2
E:123-246
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
T-cell antigen receptor
(105)
Human (Homo sapiens), alpha-chain [TaxId: 9606]
(21)
4a
d1ymmd1
D:9-104
Human (Homo sapiens), beta-chain [TaxId: 9606]
(29)
5a
d1ymme1
E:1-119
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)
Mouse (Mus musculus), I-AU [TaxId: 10090]
(12)
6a
d1ymma2
A:13-81
Protein domain
:
Class II MHC beta chain, N-terminal domain
(70)
Human (Homo sapiens), HLA-DR2 [TaxId: 9606]
(13)
7a
d1ymmb2
B:3-92
[
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]
CATH Domains
(2, 7)
Info
all CATH domains
1a: CATH_1ymmB01 (B:3-91)
1b: CATH_1ymmA01 (A:2-81)
2a: CATH_1ymmD00 (D:9-104)
2b: CATH_1ymmA02 (A:82-183)
2c: CATH_1ymmE02 (E:120-246)
2d: CATH_1ymmB02 (B:92-189)
2e: CATH_1ymmE01 (E:3-119)
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)
(
)
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
1ymmB01
B:3-91
1b
1ymmA01
A:2-81
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1ymmD00
D:9-104
2b
1ymmA02
A:82-183
2c
1ymmE02
E:120-246
2d
1ymmB02
B:92-189
2e
1ymmE01
E:3-119
[
close CATH info
]
Pfam Domains
(4, 6)
Info
all PFAM domains
1a: PFAM_C1_set_1ymmB01 (B:103-185)
1b: PFAM_C1_set_1ymmA01 (A:93-175)
1c: PFAM_C1_set_1ymmE01 (E:133-226)
2a: PFAM_MHC_II_alpha_1ymmA02 (A:4-84)
3a: PFAM_MHC_II_beta_1ymmB02 (B:13-87)
4a: PFAM_Myelin_MBP_1ymmC01 (C:85-98)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-1ymmB01
B:103-185
1b
C1-set-1ymmA01
A:93-175
1c
C1-set-1ymmE01
E:133-226
Clan
:
MHC
(252)
Family
:
MHC_II_alpha
(42)
Homo sapiens (Human)
(26)
2a
MHC_II_alpha-1ymmA02
A:4-84
Family
:
MHC_II_beta
(39)
Homo sapiens (Human)
(25)
3a
MHC_II_beta-1ymmB02
B:13-87
Clan
:
no clan defined [family: Myelin_MBP]
(2)
Family
:
Myelin_MBP
(2)
Homo sapiens (Human)
(2)
4a
Myelin_MBP-1ymmC01
C:85-98
[
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