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1QLF
Asym. Unit
Info
Asym.Unit (74 KB)
Biol.Unit 1 (69 KB)
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(1)
Title
:
MHC CLASS I H-2DB COMPLEXED WITH GLYCOPEPTIDE K3G
Authors
:
J. Tormo, E. Y. Jones
Date
:
30 Aug 99 (Deposition) - 01 Sep 99 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Immune System/Peptide, Murine Class I Mhc-Peptide Complex, Mhc, Glycopeptide, Antigen, Histocompatibility, Immunology, Immune System-Peptide Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Glithero, J. Tormo, J. S. Haurum, G. Arsequell, G. Valencia, J. Edwards, S. Springer, A. Townsend, Y. -L. Pao, M. Wormald, R. A. Dwek E. Y. Jones, T. Elliot
Crystal Structures Of Two H-2Db/Glycopeptide Complexes Suggest A Molecular Basis For Ctl Cross-Reactivity
Immunity V. 10 63 1999
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SO4
1
Ligand/Ion
SULFATE ION
[
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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
SER C:4 , ASN C:5 , TYR C:6
BINDING SITE FOR RESIDUE NAG D 400
2
AC2
SOFTWARE
ARG A:121 , ILE B:1 , HOH A:426
BINDING SITE FOR RESIDUE SO4 D 300
3
AC3
SOFTWARE
PHE A:8 , TYR A:27 , ASN A:30 , PHE B:56 , TYR B:63
BINDING SITE FOR RESIDUE GOL D 100
4
AC4
SOFTWARE
TRP A:167 , ARG A:170
BINDING SITE FOR RESIDUE GOL D 200
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_076691 (D76N, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_076691
D
96
N
B2MG_HUMAN
Disease (AMYL8)
398122820
B
D
76
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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]
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
HA11_MOUSE
281-287
1
A:257-263
[
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Exons
(3, 3)
Info
All Exons
Exon 1.1a (B:1-3)
Exon 1.2a (B:3-96)
Exon 1.4 (B:96-99)
View:
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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
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:1-3
3
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
-
-
[
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SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1qlfb_ (B:)
2a: SCOP_d1qlfa1 (A:182-276)
3a: SCOP_d1qlfa2 (A:1-181)
View:
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Classes
(
)
(
)
Folds
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(
)
Superfamilies
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)
(
)
Families
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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
d1qlfb_
B:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Mouse (Mus musculus) [TaxId: 10090]
(102)
2a
d1qlfa1
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)
Mouse (Mus musculus), H-2DB [TaxId: 10090]
(25)
3a
d1qlfa2
A:1-181
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1qlfA01 (A:1-181)
2a: CATH_1qlfB00 (B:1-99)
2b: CATH_1qlfA02 (A:182-272)
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Classes
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)
(
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Architectures
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)
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)
Topologies
(
)
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)
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)
Mouse (Mus musculus)
(40)
1a
1qlfA01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Mouse (Mus musculus)
(152)
2a
1qlfB00
B:1-99
2b
1qlfA02
A:182-272
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Pfam Domains
(4, 4)
Info
all PFAM domains
1a: PFAM_C1_set_1qlfB01 (B:11-92)
2a: PFAM_C1_set_1qlfA01 (A:189-271)
3a: PFAM_MHC_I_1qlfA02 (A:1-179)
4a: PFAM_Paramyxo_ncap_1qlfC01 (C:1-9)
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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-1qlfB01
B:11-92
Mus musculus (Mouse)
(118)
2a
C1-set-1qlfA01
A:189-271
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Mus musculus (Mouse)
(60)
3a
MHC_I-1qlfA02
A:1-179
Clan
:
Nucleocapsid
(2)
Family
:
Paramyxo_ncap
(2)
Sendai virus (strain Enders) (SeV)
(1)
4a
Paramyxo_ncap-1qlfC01
C:1-9
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Protein
Nucleic
Backbone
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Hetero
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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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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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