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3ARB
Asym. Unit
Info
Asym.Unit (293 KB)
Biol.Unit 1 (284 KB)
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(1)
Title
:
TERNARY CRYSTAL STRUCTURE OF THE NKT TCR-CD1D-ALPHA-GALACTOSYLCERAMIDE ANALOGUE-OCH
Authors
:
K. S. Wun, J. Rossjohn
Date
:
26 Nov 10 (Deposition) - 30 Mar 11 (Release) - 29 Jan 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Mouse Nkt Tcr, Mouse Cd1D, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. S. Wun, G. Cameron, O. Patel, S. S. Pang, D. G. Pellicci, L. C. Sullivan, S. Keshipeddy, M. H. Young, A. P. Uldrich, M. S. Thakur, S. K. Richardson, A. R. Howell, P. A. Illarionov, A. G. Brooks, G. S. Besra, J. Mccluskey, L. Gapin, S. A. Porcelli, D. I. Godfrey, J. Rossjohn
A Molecular Basis For The Exquisite Cd1D-Restricted Antigen Specificity And Functional Responses Of Natural Killer T Cells
Immunity V. 34 327 2011
[
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: DODECANE (D12a)
2a: N-{(1S,2S,3R)-1-[(ALPHA-D-GALACTOP... (FEEa)
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)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
D12
1
Ligand/Ion
DODECANE
2
FEE
1
Ligand/Ion
N-{(1S,2S,3R)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYOCTYL}TETRACOSANAMIDE
3
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
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Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:20 , TRP A:23 , NAG A:401
BINDING SITE FOR RESIDUE NAG A 400
02
AC2
SOFTWARE
NAG A:400
BINDING SITE FOR RESIDUE NAG A 401
03
AC3
SOFTWARE
TRP A:23 , SER A:24 , ASN A:42 , NAG A:315
BINDING SITE FOR RESIDUE NAG A 314
04
AC4
SOFTWARE
NAG A:314
BINDING SITE FOR RESIDUE NAG A 315
05
AC5
SOFTWARE
GLN A:161 , ASN A:165 , HOH A:320 , NAG A:502
BINDING SITE FOR RESIDUE NAG A 501
06
AC6
SOFTWARE
TRP A:129 , NAG A:501
BINDING SITE FOR RESIDUE NAG A 502
07
AC7
SOFTWARE
LYS A:185 , ASP A:242 , GLU A:243
BINDING SITE FOR RESIDUE PEG A 303
08
AC8
SOFTWARE
ASN A:110
BINDING SITE FOR RESIDUE NAG A 551
09
AC9
SOFTWARE
GLN A:14 , PHE A:70 , VAL A:72 , TYR A:73 , SER A:76 , ASP A:80 , TRP A:133 , ASP A:153 , GLY A:155 , THR A:156 , HOH A:310 , PRO C:28 , ASN C:30 , ARG C:95 , GLY C:96
BINDING SITE FOR RESIDUE FEE A 601
10
BC1
SOFTWARE
MET A:88
BINDING SITE FOR RESIDUE D12 A 611
11
BC2
SOFTWARE
ARG A:11 , SER A:101 , PHE B:56 , SER B:57 , LYS B:58 , TRP B:60
BINDING SITE FOR RESIDUE PEG B 100
[
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]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_B2MG_MOUSE_002 (H34Q, chain B, )
2: VAR_B2MG_MOUSE_003 (K44E, chain B, )
3: VAR_B2MG_MOUSE_004 (R81T, chain B, )
4: VAR_B2MG_MOUSE_005 (A85D, chain B, )
5: VAR_B2MG_MOUSE_006 (A85V, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_B2MG_MOUSE_002
*
H
54
Q
B2MG_MOUSE
---
---
B
H
34
Q
2
UniProt
VAR_B2MG_MOUSE_003
*
K
64
E
B2MG_MOUSE
---
---
B
K
44
E
3
UniProt
VAR_B2MG_MOUSE_004
*
R
101
T
B2MG_MOUSE
---
---
B
R
81
T
4
UniProt
VAR_B2MG_MOUSE_005
*
A
105
D
B2MG_MOUSE
---
---
B
A
85
D
5
UniProt
VAR_B2MG_MOUSE_006
*
A
105
V
B2MG_MOUSE
---
---
B
A
85
V
* ID not provided by source
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)
;
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_MOUSE
98-104
1
B:78-84
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(5, 7)
Info
All SCOP Domains
1a: SCOP_d3arbc1 (C:1-117)
1b: SCOP_d3arbd1 (D:3-118)
2a: SCOP_d3arbc2 (C:118-207)
2b: SCOP_d3arbd2 (D:119-247)
3a: SCOP_d3arbb_ (B:)
4a: SCOP_d3arba2 (A:186-302)
5a: SCOP_d3arba1 (A:6-185)
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)
(
)
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(
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(
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d3arbc1
C:1-117
1b
d3arbd1
D:3-118
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d3arbc2
C:118-207
2b
d3arbd2
D:119-247
Protein domain
:
beta2-microglobulin
(530)
Mouse (Mus musculus) [TaxId: 10090]
(166)
3a
d3arbb_
B:
Protein domain
:
CD1, alpha-3 domain
(24)
Mouse (Mus musculus) [TaxId: 10090]
(9)
4a
d3arba2
A:186-302
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)
Mouse (Mus musculus) [TaxId: 10090]
(19)
5a
d3arba1
A:6-185
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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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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Asym.Unit (293 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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