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Download EndnoteStructure-function analysis of sphingamides
Zajonc, D.M., Wang, J.To be published.
6C6C
Structure of glycolipid aGSA[20,6P] in complex with mouse CD1d
- DOI: 10.2210/pdb6C6C/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda
- Deposited: 2018-01-18 Released: 2019-01-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.08 Å
- R-Value Free: 0.241
- R-Value Work: 0.200
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Antigen-presenting glycoprotein CD1d1 | A | 285 | Mus musculus | Mutation(s): 0 Gene Names: Cd1d1 |
Find proteins for A0A0R4J090 (Mus musculus) Go to UniProtKB: A0A0R4J090 | ||||
Entity ID: 2 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Beta-2-microglobulin | B | 99 | Mus musculus | Mutation(s): 0 Gene Names: B2m |
Find proteins for P01887 (Mus musculus) Go to UniProtKB: P01887 | ||||
Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NA Query on NA | A, B | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | Ligand Interaction | |
| MAN Query on MAN | A | ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N |  | Ligand Interaction | |
| FUC Query on FUC | A | ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N |  | Ligand Interaction | |
| BMA Query on BMA | A | BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N |  | Ligand Interaction | |
| EMG Query on EMG | A | N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl)amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octan-2-yl]icosanamide aGSA[20,6P] C46 H82 N2 O10 XSVXHEMLPLUNSG-DOWKDNTMSA-N |  | Ligand Interaction | |
| NAG Query on NAG | A | N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.08 Å
- R-Value Free: 0.241
- R-Value Work: 0.200
- Space Group: P 1 21 1
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 41.525 | α = 90.00 |
| b = 98.339 | β = 106.25 |
| c = 55.310 | γ = 90.00 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Deposited Date: 2018-01-18
- Released Date: 2019-01-30
- Deposition Author(s): Zajonc, D.M., Wang, J.
Revision History
- Version 1.0: 2019-01-30
Type: Initial release
