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1OGT
Asym. Unit
Info
Asym.Unit (177 KB)
Biol.Unit 1 (170 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HLA-B*2705 COMPLEXED WITH THE VASOACTIVE INTESTINAL PEPTIDE TYPE 1 RECEPTOR (VIPR) PEPTIDE (RESIDUES 400-408)
Authors
:
M. Hulsmeyer, M. T. Fiorillo, F. Bettosini, R. Sorrentino, W. Saenger, A. Ziegler, B. Uchanska-Ziegler
Date
:
13 May 03 (Deposition) - 29 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.47
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Immune System/Complex, Immune System, Mhc (Major Histocompatibility Complex), Hla- B*2705
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Hulsmeyer, M. T. Fiorillo, F. Bettosini, R. Sorrentino, W. Saenger, A. Ziegler, B. Uchanska-Ziegler
Dual, Hla-B27 Subtype-Dependent Conformation Of A Self-Peptide
J. Exp. Med. V. 199 271 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
2a: MANGANESE (II) ION (MNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
5
Ligand/Ion
GLYCEROL
2
MN
1
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:76 , HIS A:197 , HOH A:2204 , HOH A:2485 , HOH A:2486 , HOH A:2487 , HIS C:8
BINDING SITE FOR RESIDUE MN A1279
2
AC2
SOFTWARE
TYR A:27 , ASP A:29 , ASP A:30 , HOH A:2012 , HOH A:2478 , HOH A:2479 , HOH A:2481 , TYR B:63 , HOH B:2149
BINDING SITE FOR RESIDUE GOL A1277
3
AC3
SOFTWARE
GLN A:141 , GLN A:144 , ARG A:145 , HOH A:2483
BINDING SITE FOR RESIDUE GOL A1278
4
AC4
SOFTWARE
PRO A:235 , HOH A:2061 , SER B:52 , TYR B:63 , HOH B:2132 , HOH B:2198 , HOH B:2199 , HOH B:2200 , HOH B:2201 , HOH B:2202
BINDING SITE FOR RESIDUE GOL B1100
5
AC5
SOFTWARE
ILE A:66 , ALA A:69 , ASP A:196 , HOH A:2186 , TRP C:4 , ARG C:6 , HOH C:2023 , HOH C:2032
BINDING SITE FOR RESIDUE GOL C1010
6
AC6
SOFTWARE
ARG A:62 , HOH A:2343 , HOH A:2454 , TRP C:4
BINDING SITE FOR RESIDUE GOL C1011
[
close Site info
]
SAPs(SNPs)/Variants
(12, 12)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_056341 (A41T, chain A, )
02: VAR_016379 (Y59H, chain A, )
03: VAR_016380 (D77N, chain A, )
04: VAR_016381 (D77S, chain A, )
05: VAR_016383 (T80N, chain A, )
06: VAR_016385 (N97S, chain A, )
07: VAR_016387 (H114D, chain A, )
08: VAR_016388 (D116H, chain A, )
09: VAR_016389 (D116Y, chain A, )
10: VAR_016390 (S131R, chain A, )
11: VAR_016391 (V152E, chain A, )
12: VAR_016392 (A211G, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_056341
A
65
T
1B27_HUMAN
Polymorphism
1050529
A
A
41
T
02
UniProt
VAR_016379
Y
83
H
1B27_HUMAN
Polymorphism
---
A
Y
59
H
03
UniProt
VAR_016380
D
101
N
1B27_HUMAN
Polymorphism
---
A
D
77
N
04
UniProt
VAR_016381
D
101
S
1B27_HUMAN
Polymorphism
---
A
D
77
S
05
UniProt
VAR_016383
T
104
N
1B27_HUMAN
Polymorphism
---
A
T
80
N
06
UniProt
VAR_016385
N
121
S
1B27_HUMAN
Polymorphism
---
A
N
97
S
07
UniProt
VAR_016387
H
138
D
1B27_HUMAN
Polymorphism
---
A
H
114
D
08
UniProt
VAR_016388
D
140
H
1B27_HUMAN
Polymorphism
---
A
D
116
H
09
UniProt
VAR_016389
D
140
Y
1B27_HUMAN
Polymorphism
---
A
D
116
Y
10
UniProt
VAR_016390
S
155
R
1B27_HUMAN
Polymorphism
---
A
S
131
R
11
UniProt
VAR_016391
V
176
E
1B27_HUMAN
Polymorphism
---
A
V
152
E
12
UniProt
VAR_016392
A
235
G
1B27_HUMAN
Polymorphism
---
A
A
211
G
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,B:78-84,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_GORGO
98-104
1
B:78-84
B2MG_HUMAN
98-104
1
B:78-84
B2MG_PANTR
98-104
1
B:78-84
1B27_HUMAN
281-287
1
A:257-263
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.1a (B:0-3)
Exon 1.2a (B:3-96)
Exon 1.4 (B:96-99)
Exon 2.18c (C:1-9)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2a
3: Boundary 1.2a/1.4
4: Boundary 1.4/1.5
5: Boundary 2.17/2.18c
6: Boundary 2.18c/-
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
1.1a
ENSPTRT00000012956
1a
ENSPTRE00000370636
chr15:
41860468-41860604
137
B2MG_PANTR
1-23
23
1
B:0-3
4
1.2a
ENSPTRT00000012956
2a
ENSPTRE00000238527
chr15:
41864413-41864691
279
B2MG_PANTR
23-116
94
1
B:3-96
94
1.4
ENSPTRT00000012956
4
ENSPTRE00000238528
chr15:
41865318-41865345
28
B2MG_PANTR
116-119
4
1
B:96-99
4
1.5
ENSPTRT00000012956
5
ENSPTRE00000070423
chr15:
41866598-41867140
543
B2MG_PANTR
-
0
0
-
-
2.5c
ENST00000325123
5c
ENSE00001297399
chr3:
42544115-42544305
191
VIPR1_HUMAN
1-26
26
0
-
-
2.7a
ENST00000325123
7a
ENSE00001727620
chr3:
42555241-42555346
106
VIPR1_HUMAN
27-62
36
0
-
-
2.8b
ENST00000325123
8b
ENSE00001805839
chr3:
42560715-42560822
108
VIPR1_HUMAN
62-98
37
0
-
-
2.9
ENST00000325123
9
ENSE00001728664
chr3:
42567379-42567485
107
VIPR1_HUMAN
98-133
36
0
-
-
2.10a
ENST00000325123
10a
ENSE00002168879
chr3:
42568885-42568988
104
VIPR1_HUMAN
134-168
35
0
-
-
2.10e
ENST00000325123
10e
ENSE00001740276
chr3:
42569483-42569615
133
VIPR1_HUMAN
168-212
45
0
-
-
2.12c
ENST00000325123
12c
ENSE00001651205
chr3:
42572271-42572424
154
VIPR1_HUMAN
213-264
52
0
-
-
2.13b
ENST00000325123
13b
ENSE00001630370
chr3:
42572963-42573023
61
VIPR1_HUMAN
264-284
21
0
-
-
2.14
ENST00000325123
14
ENSE00001645490
chr3:
42573295-42573361
67
VIPR1_HUMAN
284-306
23
0
-
-
2.15b
ENST00000325123
15b
ENSE00001611390
chr3:
42573734-42573825
92
VIPR1_HUMAN
307-337
31
0
-
-
2.16b
ENST00000325123
16b
ENSE00001789013
chr3:
42576467-42576596
130
VIPR1_HUMAN
337-380
44
0
-
-
2.17
ENST00000325123
17
ENSE00001634221
chr3:
42576835-42576876
42
VIPR1_HUMAN
381-394
14
0
-
-
2.18c
ENST00000325123
18c
ENSE00001620791
chr3:
42577582-42579059
1478
VIPR1_HUMAN
395-457
63
1
C:1-9
9
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1ogtb_ (B:)
2a: SCOP_d1ogta1 (A:182-276)
3a: SCOP_d1ogta2 (A:1-181)
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
d1ogtb_
B:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d1ogta1
A:182-276
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-B27 [TaxId: 9606]
(9)
3a
d1ogta2
A:1-181
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1ogtA01 (A:1-181)
2a: CATH_1ogtB00 (B:0-99)
2b: CATH_1ogtA02 (A:182-276)
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
1ogtA01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1ogtB00
B:0-99
2b
1ogtA02
A:182-276
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_C1_set_1ogtB01 (B:11-92)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-1ogtB01
B:11-92
[
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]
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