6CYW
Structure of sphingomyelin in complex with mouse CD1d
- PDB DOI: https://doi.org/10.2210/pdb6CYW/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2018-04-06 Released: 2019-04-10 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.256 
- R-Value Work: 0.223 
- R-Value Observed: 0.224 
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 |
Antigen-presenting glycoprotein CD1d1 | 285 | Mus musculus | Mutation(s): 0  Gene Names: Cd1d1, mCG_3074 | ||
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 | |
FO4 Query on FO4 | F [auth A] | sphingomyelin C47 H94 N2 O6 P NHYQHBPEJLFFSO-QYKFWSDSSA-O | |||
NAG Query on NAG | D [auth A], E [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: 1.95 Å
- R-Value Free: 0.256 
- R-Value Work: 0.223 
- R-Value Observed: 0.224 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 42.134 | α = 90 |
b = 105.256 | β = 90 |
c = 106.388 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Entry History 
Deposition Data
- Released Date: 2019-04-10  Deposition Author(s): Zajonc, D.M., Wang, J.
Revision History (Full details and data files)
- Version 1.0: 2019-04-10
Type: Initial release - Version 1.1: 2019-11-27
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary