2AKR
Structural basis of sulfatide presentation by mouse CD1d
- PDB DOI: https://doi.org/10.2210/pdb2AKR/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2005-08-03 Released: 2005-12-06 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.249 
- R-Value Work: 0.186 
- R-Value Observed: 0.187 
This is version 2.1 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 |
T-cell surface glycoprotein CD1d1 | 285 | Mus musculus | Mutation(s): 0  Gene Names: Cd1d1, Cd1.1 | ||
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 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-2-microglobulin | 99 | Mus musculus | Mutation(s): 0  Gene Names: B2m | ||
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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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CIS Query on CIS | I [auth A], L [auth C] | (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 | |||
NAG Query on NAG | F [auth A], G [auth A], H [auth A], J [auth C], K [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.249 
- R-Value Work: 0.186 
- R-Value Observed: 0.187 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 58.858 | α = 90 |
b = 74.843 | β = 102.1 |
c = 101.564 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
CCP4 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2005-12-06  Deposition Author(s): Zajonc, D.M., Halder, R., Wu, D., Maricic, I., Roy, K., Wong, C.-H., Kumar, V., Wilson, I.A.
Revision History (Full details and data files)
- Version 1.0: 2005-12-06
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary