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Asym. Unit
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Asym.Unit (85 KB)
Biol.Unit 1 (80 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF HLA-B*1501 IN COMPLEX WITH PEPTIDES FROM HUMAN UBCH6 AND EPSTEIN-BARR VIRUS EBNA-3
Authors
:
G. Roder, T. Blicher, B. R. Johannessen, O. Kristensen, S. Buus, M. Gajh
Date
:
14 Oct 04 (Deposition) - 14 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.79
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Major Histocompatibility Antigen, Mhc, Hla, Hla-B62, Hla-B*1501, Complex (Antigen-Peptide), Immune System-Ligase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Roder, T. Blicher, S. Justesen, B. Johannesen, O. Kristensen, J. Kastrup, S. Buus, M. Gajhede
Crystal Structures Of Two Peptide-Hla-B*1501 Complexes; Structural Characterization Of The Hla-B62 Supertype
Acta Crystallogr. , Sect. D V. 62 1300 2006
[
close entry info
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
3a: UREA (UREa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
SO4
2
Ligand/Ion
SULFATE ION
3
URE
1
Ligand/Ion
UREA
[
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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
ASP A:39 , ASN A:127 , GLU A:128 , ASP A:129 , HOH A:3039 , HOH A:3325
BINDING SITE FOR RESIDUE SO4 A 1001
2
AC2
SOFTWARE
GOL A:3001 , SER B:57 , LYS B:58 , HOH B:1009 , HOH B:1100
BINDING SITE FOR RESIDUE SO4 B 1002
3
AC3
SOFTWARE
ARG A:234 , GLN A:242 , SER B:11 , HIS B:13 , PRO B:14
BINDING SITE FOR RESIDUE URE A 2001
4
AC4
SOFTWARE
THR A:233 , PHE A:241 , HOH A:3389 , TYR B:26 , TYR B:63 , SO4 B:1002
BINDING SITE FOR RESIDUE GOL A 3001
[
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SAPs(SNPs)/Variants
(9, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016365 (A24S, chain A, )
2: VAR_016367 (E63N, chain A, )
3: VAR_016368 (S67C, chain A, )
4: VAR_016369 (S67Y, chain A, )
5: VAR_016371 (L95W, chain A, )
6: VAR_016372 (R97T, chain A, )
7: VAR_016373 (H113Y, chain A, )
8: VAR_016374 (W156L, chain A, )
9: VAR_016376 (P250L, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016365
A
48
S
1B15_HUMAN
Polymorphism
---
A
A
24
S
2
UniProt
VAR_016367
E
87
N
1B15_HUMAN
Polymorphism
---
A
E
63
N
3
UniProt
VAR_016368
S
91
C
1B15_HUMAN
Polymorphism
---
A
S
67
C
4
UniProt
VAR_016369
S
91
Y
1B15_HUMAN
Polymorphism
---
A
S
67
Y
5
UniProt
VAR_016371
L
119
W
1B15_HUMAN
Polymorphism
---
A
L
95
W
6
UniProt
VAR_016372
R
121
T
1B15_HUMAN
Polymorphism
---
A
R
97
T
7
UniProt
VAR_016373
H
137
Y
1B15_HUMAN
Polymorphism
---
A
H
113
Y
8
UniProt
VAR_016374
W
180
L
1B15_HUMAN
Polymorphism
---
A
W
156
L
9
UniProt
VAR_016376
P
274
L
1B15_HUMAN
Polymorphism
---
A
P
250
L
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
1B15_HUMAN
281-287
1
A:257-263
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Exons
(1, 1)
Info
All Exons
Exon 1.8a (C:1-9)
View:
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All Exon Boundaries
1: Boundary 1.6b/1.8a
2: Boundary 1.8a/1.10b
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
1.1a
ENST00000306627
1a
ENSE00001810272
chr3:
23847394-23847579
186
UB2E1_HUMAN
-
0
0
-
-
1.2b
ENST00000306627
2b
ENSE00002168375
chr3:
23848728-23848912
185
UB2E1_HUMAN
1-51
51
0
-
-
1.6b
ENST00000306627
6b
ENSE00001640993
chr3:
23852951-23853001
51
UB2E1_HUMAN
51-68
18
0
-
-
1.8a
ENST00000306627
8a
ENSE00001753310
chr3:
23929058-23929190
133
UB2E1_HUMAN
68-112
45
1
C:1-9
9
1.10b
ENST00000306627
10b
ENSE00001702254
chr3:
23930603-23930750
148
UB2E1_HUMAN
113-162
50
0
-
-
1.11d
ENST00000306627
11d
ENSE00001631307
chr3:
23932000-23932807
808
UB2E1_HUMAN
162-193
32
0
-
-
[
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]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1xr9b_ (B:)
2a: SCOP_d1xr9a1 (A:182-276)
3a: SCOP_d1xr9a2 (A:1-181)
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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
:
beta2-microglobulin
(530)
Human (Homo sapiens) [TaxId: 9606]
(350)
1a
d1xr9b_
B:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d1xr9a1
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-B53 [TaxId: 9606]
(23)
3a
d1xr9a2
A:1-181
[
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1xr9A01 (A:1-181)
2a: CATH_1xr9B00 (B:1-99)
2b: CATH_1xr9A02 (A:182-272)
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Classes
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)
(
)
Architectures
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)
(
)
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
1xr9A01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1xr9B00
B:1-99
2b
1xr9A02
A:182-272
[
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Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_C1_set_1xr9A01 (A:185-271)
1b: PFAM_C1_set_1xr9B01 (B:11-92)
2a: PFAM_MHC_I_1xr9A02 (A:1-179)
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Clans
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Organisms
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)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-1xr9A01
A:185-271
1b
C1-set-1xr9B01
B:11-92
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
2a
MHC_I-1xr9A02
A:1-179
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]
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Nucleic
Backbone
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Hetero
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Solvent
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Chain B
Chain C
Asymmetric Unit 1
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