5TW5
Structure of mouse CD1d with bound glycosphingolipid JJ112
- PDB DOI: https://doi.org/10.2210/pdb5TW5/pdb
- Classification: immune system/inhibitor
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes 
- Deposited: 2016-11-11 Released: 2017-09-20 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.244 
- R-Value Work: 0.213 
- R-Value Observed: 0.213 
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): 1  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 | 97 | 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 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
7LM Query on 7LM | G [auth A] | N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxy-16-phenylhexadecan-2-yl]octanamide C36 H63 N O9 YDGPBAWHWVHKQP-QNAIHFNASA-N | |||
PLM Query on PLM | D [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
NAG Query on NAG | E [auth A], F [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: 1.85 Å
- R-Value Free: 0.244 
- R-Value Work: 0.213 
- R-Value Observed: 0.213 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 42.172 | α = 90 |
b = 106.231 | β = 90 |
c = 106.892 | γ = 90 |
Software Name | Purpose |
---|---|
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
Blue | data reduction |
Entry History 
Deposition Data
- Released Date: 2017-09-20  Deposition Author(s): Zajonc, D.M., Wang, J.
Revision History (Full details and data files)
- Version 1.0: 2017-09-20
Type: Initial release - 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