Research workbench
The molecular bases of DELTA/ALPHA beta T cell-mediated antigen recognition.
Analyse The molecular bases of DELTA/ALPHA beta T cell-mediated antigen recognition. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WO4
- Type
- protein
- Length
- 813 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D; Beta-2-microglobulin; TCR variable delta 1 chain…
- UniProt
- P15813, P61769
- Ligands
- JLS, NAG, FUC, BMA
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D | protein | 273 | 27% helix, 41% strand | P15813 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 53% strand | P61769 |
| C | TCR variable delta 1 chain and TCR constant alpha | protein | 200 | 7% helix, 46% strand | — |
| D | TCR variable beta 2 (TRVB20) chain and TCR constant beta | protein | 242 | 7% helix, 52% strand | — |
Ligands and binding sites
- JLS · (15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide · ligand · chains A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.87 | 0.88 | 70 | JLS |
| 2 | 1019 | 0.72 | 0.76 | 66 | empty |
| 3 | 313 | 0.63 | 0.79 | 35 | empty |
| 4 | 268 | 0.58 | 0.78 | 44 | empty |
| 5 | 125 | 0.47 | 0.78 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2209 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1279 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 597 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 359 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · 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 P15813
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4WO4 · PDBe 4WO4 · UniProt P15813 · UniProt P61769
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