Research workbench
Structure of alpha-GSA[8,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR
Analyse Structure of alpha-GSA[8,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CWE
- Type
- protein
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Mus musculus
- Molecule
- Antigen-presenting glycoprotein CD1d1; Beta-2-microglobulin; Chimeric T cell antigen…
- UniProt
- A0A0R4J090, P01887
- Ligands
- 7LP, PLM, NAG, FUC
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.2 · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1d1 | protein | 267 | 27% helix, 40% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| C | Chimeric T cell antigen receptor alpha chain Va14,Va24,Ja18 | protein | 199 | 5% helix, 48% strand | — |
| D | Chimeric T cell antigen receptor beta chain Vb8.2, vb11 | protein | 239 | 6% helix, 49% strand | — |
Ligands and binding sites
- 7LP · (5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide · ligand · chains A, C
- PLM · Palmitic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.86 | 0.87 | 74 | 7LP, PLM |
| 2 | 903 | 0.69 | 0.75 | 67 | empty |
| 3 | 414 | 0.65 | 0.79 | 48 | empty |
| 4 | 184 | 0.50 | 0.77 | 23 | empty |
| 5 | 92 | 0.42 | 0.78 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2190 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1257 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 359 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6CWE · Structure of alpha-GSA[8,6P] bound by CD1D and in complex with the VA14VB8.2 TCR · the same entry in another collection · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A0R4J090
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6CWE · PDBe 6CWE · UniProt A0A0R4J090 · UniProt P01887
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