1Z5L
Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1D
- PDB DOI: https://doi.org/10.2210/pdb1Z5L/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Drosophila melanogaster
- Mutation(s): No 
- Deposited: 2005-03-18 Released: 2005-07-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.294 
- R-Value Work: 0.242 
- R-Value Observed: 0.243 
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 |
T-cell surface glycoprotein CD1d antigen | 285 | Mus musculus | Mutation(s): 0  | ||
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  | ||
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 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PBS Query on PBS | I [auth A], L [auth C] | (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL C32 H63 N O9 PFXOKSFCNLTBGK-YFWOXBOYSA-N | |||
R16 Query on R16 | J [auth A], M [auth C] | HEXADECANE C16 H34 DCAYPVUWAIABOU-UHFFFAOYSA-N | |||
NAG Query on NAG | G [auth A], H [auth A], 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: 2.20 Å
- R-Value Free: 0.294 
- R-Value Work: 0.242 
- R-Value Observed: 0.243 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 59.451 | α = 90 |
b = 77.045 | β = 107.63 |
c = 111.014 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
CCP4 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2005-07-19  Deposition Author(s): Zajonc, D.M., Cantu, C., Mattner, J., Zhou, D., Savage, P.B., Bendelac, A., Wilson, I.A., Teyton, L.
Revision History (Full details and data files)
- Version 1.0: 2005-07-19
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-08-23
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary