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1GZP
Asym. Unit
Info
Asym.Unit (72 KB)
Biol.Unit 1 (65 KB)
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(1)
Title
:
CD1B IN COMPLEX WITH GM2 GANGLIOSIDE
Authors
:
S. D. Gadola, N. R. Zaccai, K. Harlos, D. Shepherd, G. Ritter, R. R. Schmidt, E. Y. Jones, V. Cerundolo
Date
:
24 May 02 (Deposition) - 31 Jul 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Lipid, Ganglioside, Mhc, Antigen Presentation, Glycoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. D. Gadola, N. R. Zaccai, K. Harlos, D. Shepherd, J. C. Castro-Palomino, G. Ritter, R. R. Schmidt, E. Y. Jones, V. Cerundolo
Structure Of Human Cd1B With Bound Ligands At 2. 3 A, A Maze For Alkyl Chains
Nat. Immunol. V. 3 721 2002
[
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: DODECANE (D12a)
2a: N-[(1S,2S)-2-HYDROXY-1-({[(2R,3R,4... (GM2a)
3a: DOCOSANE (TWTa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
D12
1
Ligand/Ion
DODECANE
2
GM2
1
Ligand/Ion
N-[(1S,2S)-2-HYDROXY-1-({[(2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]OXY}METHYL)OCTADECYL]OCTADECANAMIDE
3
TWT
1
Ligand/Ion
DOCOSANE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:73 , GLY A:76 , GLY A:153 , ILE A:154 , MET A:155 , THR A:157 , LEU A:161 , D12 A:1281
BINDING SITE FOR RESIDUE GM2 A1280
2
AC2
SOFTWARE
GLU A:80 , MET A:90 , GM2 A:1280
BINDING SITE FOR RESIDUE D12 A1281
3
AC3
SOFTWARE
ILE A:13 , GLN A:14 , TYR A:73 , ALA A:100 , PHE A:123
BINDING SITE FOR RESIDUE TWT A1282
[
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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, 1)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84,B:78-84,B:78-84)
;
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
[
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Exons
(7, 7)
Info
All Exons
Exon 1.1a (B:0-3)
Exon 1.2a (B:3-96)
Exon 1.4 (B:96-99)
Exon 2.2a (A:4-92)
Exon 2.3 (A:92-185)
Exon 2.4b (A:185-278)
Exon 2.5 (A:278-280 (gaps))
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
5: Boundary 2.1/2.2a
6: Boundary 2.2a/2.3
7: Boundary 2.3/2.4b
8: Boundary 2.4b/2.5
9: Boundary 2.5/2.6a
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
-
-
2.1
ENST00000368168
1
ENSE00001446457
chr1:
158301321-158301153
169
CD1B_HUMAN
1-21
21
0
-
-
2.2a
ENST00000368168
2a
ENSE00001039203
chr1:
158300852-158300586
267
CD1B_HUMAN
21-110
90
1
A:4-92
89
2.3
ENST00000368168
3
ENSE00001039193
chr1:
158299920-158299642
279
CD1B_HUMAN
110-203
94
1
A:92-185
94
2.4b
ENST00000368168
4b
ENSE00001039201
chr1:
158299438-158299160
279
CD1B_HUMAN
203-296
94
1
A:185-278
94
2.5
ENST00000368168
5
ENSE00001039199
chr1:
158298804-158298711
94
CD1B_HUMAN
296-327
32
1
A:278-280 (gaps)
17
2.6a
ENST00000368168
6a
ENSE00001598880
chr1:
158298047-158297741
307
CD1B_HUMAN
327-333
7
0
-
-
[
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SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1gzpb_ (B:)
2a: SCOP_d1gzpa1 (A:184-280)
3a: SCOP_d1gzpa2 (A:4-183)
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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
d1gzpb_
B:
Protein domain
:
CD1, alpha-3 domain
(24)
Human (Homo sapiens), CD1b [TaxId: 9606]
(6)
2a
d1gzpa1
A:184-280
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
:
CD1, alpha-1 and alpha-2 domains
(39)
Human (Homo sapiens), CD1b [TaxId: 9606]
(6)
3a
d1gzpa2
A:4-183
[
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1gzpA01 (A:7-182)
2a: CATH_1gzpB00 (B:0-99)
2b: CATH_1gzpA02 (A:183-278)
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)
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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)
Human (Homo sapiens)
(249)
1a
1gzpA01
A:7-182
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1gzpB00
B:0-99
2b
1gzpA02
A:183-278
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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