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2PO6
Asym. Unit
Info
Asym.Unit (274 KB)
Biol.Unit 1 (135 KB)
Biol.Unit 2 (134 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CD1D-LIPID-ANTIGEN COMPLEXED WITH BETA-2-MICROGLOBULIN, NKT15 ALPHA-CHAIN AND NKT15 BETA-CHAIN
Authors
:
N. A. Borg
Date
:
25 Apr 07 (Deposition) - 03 Jul 07 (Release) - 29 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Cd1D-Lipid Antigen Nkt15 Complex, Lipid Binding Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. A. Borg, K. S. Wun, L. Kjer-Nielsen, M. C. Wilce, D. G. Pellicci, R. Koh, G. S. Besra, M. Bharadwaj, D. I. Godfrey, J. Mccluskey, J. Rossjohn
Cd1D-Lipid-Antigen Recognition By The Semi-Invariant Nkt T-Cell Receptor.
Nature V. 448 44 2007
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOP... (AGHa)
1b: N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOP... (AGHb)
2a: BETA-D-MANNOSE (BMAa)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AGH
2
Ligand/Ion
N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
2
BMA
1
Ligand/Ion
BETA-D-MANNOSE
3
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:24 , ASN A:42 , NAG A:1100
BINDING SITE FOR RESIDUE NAG A 1000
2
AC2
SOFTWARE
NAG A:1000 , BMA A:1200
BINDING SITE FOR RESIDUE NAG A 1100
3
AC3
SOFTWARE
NAG A:1100
BINDING SITE FOR RESIDUE BMA A 1200
4
AC4
SOFTWARE
ALA A:19 , ASN A:20 , TRP A:23
BINDING SITE FOR RESIDUE NAG A 2000
5
AC5
SOFTWARE
ASN E:20 , SER E:22 , NAG E:3100
BINDING SITE FOR RESIDUE NAG E 3000
6
AC6
SOFTWARE
TRP E:23 , NAG E:3000
BINDING SITE FOR RESIDUE NAG E 3100
7
AC7
SOFTWARE
THR E:24 , ASN E:42 , ASP E:43
BINDING SITE FOR RESIDUE NAG E 4000
8
AC8
SOFTWARE
CYS A:12 , LEU A:29 , HIS A:38 , TRP A:40 , PHE A:70 , TYR A:73 , SER A:76 , PHE A:77 , ASP A:80 , LEU A:90 , ASP A:151 , TRP A:153 , THR A:154 , PRO C:28 , PHE C:29 , SER C:30 , ARG C:95 , GLY C:96
BINDING SITE FOR RESIDUE AGH C 208
9
AC9
SOFTWARE
LEU E:13 , GLN E:14 , TRP E:40 , TYR E:73 , SER E:76 , PHE E:77 , ASP E:80 , PHE E:84 , LEU E:90 , PHE E:118 , ASP E:151 , TRP E:153 , THR E:154 , PHE E:169 , PHE G:29 , SER G:30 , ARG G:95 , GLY G:96
BINDING SITE FOR RESIDUE AGH E 2
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_010211 (T46S, chain A/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_010211
T
64
S
CD1D_HUMAN
Polymorphism
62621276
A/E
T
46
S
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,F: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_HUMAN
98-104
2
B:78-84
F:78-84
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Exons
(4, 7)
Info
All Exons
Exon 1.3 (A:6-92 | E:6-92)
Exon 1.4 (A:92-185 | E:92-185)
Exon 1.5 (A:185-278 | E:185-277)
Exon 1.6 (A:278-280 | -)
View:
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All Exon Boundaries
1: Boundary 1.2/1.3
2: Boundary 1.3/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6
5: Boundary 1.6/1.7
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
1.1
ENST00000368171
1
ENSE00001208284
chr1:
158149737-158149952
216
CD1D_HUMAN
-
0
0
-
-
1.2
ENST00000368171
2
ENSE00001446474
chr1:
158150609-158150952
344
CD1D_HUMAN
1-21
21
0
-
-
1.3
ENST00000368171
3
ENSE00001039119
chr1:
158151245-158151511
267
CD1D_HUMAN
21-110
90
2
A:6-92
E:6-92
87
87
1.4
ENST00000368171
4
ENSE00001039117
chr1:
158151822-158152100
279
CD1D_HUMAN
110-203
94
2
A:92-185
E:92-185
94
94
1.5
ENST00000368171
5
ENSE00001690740
chr1:
158152668-158152946
279
CD1D_HUMAN
203-296
94
2
A:185-278
E:185-277
94
93
1.6
ENST00000368171
6
ENSE00001308386
chr1:
158153726-158153825
100
CD1D_HUMAN
296-329
34
1
A:278-280
-
3
-
1.7
ENST00000368171
7
ENSE00001446472
chr1:
158153919-158154686
768
CD1D_HUMAN
329-335
7
0
-
-
[
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SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2po6b1 (B:1-99)
1b: SCOP_d2po6f1 (F:2-99)
2a: SCOP_d2po6a1 (A:184-277)
2b: SCOP_d2po6e1 (E:184-277)
3a: SCOP_d2po6a2 (A:6-183)
3b: SCOP_d2po6e2 (E:6-183)
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Superfamilies
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(
)
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
d2po6b1
B:1-99
1b
d2po6f1
F:2-99
Protein domain
:
CD1, alpha-3 domain
(24)
Human (Homo sapiens), CD1d [TaxId: 9606]
(2)
2a
d2po6a1
A:184-277
2b
d2po6e1
E:184-277
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), CD1d [TaxId: 9606]
(2)
3a
d2po6a2
A:6-183
3b
d2po6e2
E:6-183
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2po6A01 (A:6-182)
1b: CATH_2po6E01 (E:6-182)
2a: CATH_2po6B00 (B:1-99)
2b: CATH_2po6C01 (C:1-116)
2c: CATH_2po6G01 (G:1-116)
2d: CATH_2po6D01 (D:2-118)
2e: CATH_2po6H01 (H:2-118)
2f: CATH_2po6D02 (D:119-244)
2g: CATH_2po6H02 (H:119-244)
2h: CATH_2po6A02 (A:183-280)
2i: CATH_2po6E02 (E:183-277)
2j: CATH_2po6F00 (F:2-99)
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)
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)
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(
)
(
)
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
2po6A01
A:6-182
1b
2po6E01
E:6-182
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2po6B00
B:1-99
2b
2po6C01
C:1-116
2c
2po6G01
G:1-116
2d
2po6D01
D:2-118
2e
2po6H01
H:2-118
2f
2po6D02
D:119-244
2g
2po6H02
H:119-244
2h
2po6A02
A:183-280
2i
2po6E02
E:183-277
2j
2po6F00
F:2-99
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_C1_set_2po6F01 (F:11-92)
1b: PFAM_C1_set_2po6F02 (F:11-92)
1c: PFAM_C1_set_2po6E01 (E:194-274)
1d: PFAM_C1_set_2po6E02 (E:194-274)
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)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-2po6F01
F:11-92
1b
C1-set-2po6F02
F:11-92
1c
C1-set-2po6E01
E:194-274
1d
C1-set-2po6E02
E:194-274
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Asym.Unit (274 KB)
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