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Download EndnoteGlycolipid recognition by iNKT cells
Wang, J., Zajonc, D.M.To be published.
5VCJ
Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR
- DOI: 10.2210/pdb5VCJ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
- Mutation(s): 1
- Deposited: 2017-03-31 Released: 2018-04-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.16 Å
- R-Value Free: 0.248
- R-Value Work: 0.189
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): 1 Gene Names: Cd1d1 (Cd1.1) |
Find proteins for P11609 (Mus musculus) Go to UniProtKB: P11609 | ||||
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 | ||||
Entity ID: 3 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain) | C | 209 | N/A | Mutation(s): 0 |
| Protein Feature View is not available: No corresponding UniProt sequence found. | ||||
Entity ID: 4 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain) | D | 241 | N/A | Mutation(s): 0 |
| Protein Feature View is not available: No corresponding UniProt sequence found. | ||||
Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PBS Query on PBS | A | (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL C32 H63 N O9 PFXOKSFCNLTBGK-YFWOXBOYSA-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 | |
| NAG Query on NAG | A | N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | Ligand Interaction | |
| PLM Query on PLM | A | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.16 Å
- R-Value Free: 0.248
- R-Value Work: 0.189
- Space Group: C 2 2 21
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 79.261 | α = 90.00 |
| b = 191.611 | β = 90.00 |
| c = 151.249 | γ = 90.00 |
| Software Name | Purpose |
|---|---|
| PHASER | phasing |
| HKL | data reduction |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| REFMAC | refinement |
Entry History
Deposition Data
- Deposited Date: 2017-03-31
- Released Date: 2018-04-04
- Deposition Author(s): Wang, J., Zajonc, D.M.
Revision History
- Version 1.0: 2018-04-04
Type: Initial release
