4IRJ
Structure of the mouse CD1d-4ClPhC-alpha-GalCer-iNKT TCR complex
- PDB DOI: https://doi.org/10.2210/pdb4IRJ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, Homo sapiens
- Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2013-01-14 Released: 2013-08-28 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.228 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Antigen-presenting glycoprotein CD1d1 | 285 | Mus musculus | Mutation(s): 0  Gene Names: Cd1.1, CD1d, Cd1d1 | ||
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 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-2-microglobulin | 99 | Mus musculus | Mutation(s): 0  Gene Names: B2m, beta-2-microglobulin | ||
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 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Valpha14 (mouse variable domain, human constant domain) | 209 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 0  Gene Names: Valpha14 (mouse variable domain, human constant domain) | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Vbeta8.2 (mouse variable domain, human constant domain) | 241 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 0  Gene Names: Vbeta8.2 (mouse variable domain, human constant domain) | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
1L9 Query on 1L9 | H [auth A] | N-[(2S,3S,4R)-1-({6-O-[(4-chlorophenyl)carbamoyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide C57 H103 Cl N2 O10 MAGJZLBUXUBUBN-FNBNLLHXSA-N | |||
NAG Query on NAG | F [auth A], G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.228 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 79.283 | α = 90 |
b = 191.862 | β = 90 |
c = 151.598 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
Entry History 
Deposition Data
- Released Date: 2013-08-28  Deposition Author(s): Nemcovic, M., Zajonc, D.M.
Revision History (Full details and data files)
- Version 1.0: 2013-08-28
Type: Initial release - Version 1.1: 2013-09-04
Changes: Database references - Version 1.2: 2014-02-05
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary