4APQ
Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide
- PDB DOI: https://doi.org/10.2210/pdb4APQ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Trichoplusia ni, Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2012-04-05 Released: 2013-04-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.232 
- R-Value Work: 0.177 
- R-Value Observed: 0.180 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1 | 302 | Mus musculus | Mutation(s): 1  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609 | |||||
IMPC:  MGI:107674 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P11609 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
BETA-2-MICROGLOBULIN | 99 | Mus musculus | Mutation(s): 1  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887 | |||||
IMPC:  MGI:88127 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01887 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
MOUSE NKT TCR VALPHA14, HUMAN NKT TCR VALPHA14 | 207 | Mus musculus | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848 | |||||
PHAROS:  P01848 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01848 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
MOUSE NKT TCR AUTOREACTIVE-VBETA6, HUMAN NKT TCR AUTOREACTIVE-VBETA6 | 243 | Mus musculus | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G08918EL GlyCosmos:  G08918EL GlyGen:  G08918EL |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CIS Query on CIS | H [auth A] | (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE C48 H91 N O11 S ZZQWQNAZXFNSEP-JCOQVFCVSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.232 
- R-Value Work: 0.177 
- R-Value Observed: 0.180 
- Space Group: P 41 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 95.11 | α = 90 |
b = 95.11 | β = 90 |
c = 291.4 | γ = 90 |
Software Name | Purpose |
---|---|
BUSTER | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2013-04-24  Deposition Author(s): Clarke, A.J., Le Nours, J., Rossjohn, J.
Revision History (Full details and data files)
- Version 1.0: 2013-04-24
Type: Initial release - Version 1.1: 2018-06-20
Changes: Data collection, Derived calculations - Version 1.2: 2019-04-03
Changes: Data collection, Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary