MolNFT v1 · #109215 · protein
Crystal structure of human TCR alpha chain-TRAV21-TRAJ8, beta chain- TRBV7-8, antigen-presenting glycoprotein CD1D, and beta-2- microglobulin
4WW2: “Crystal structure of human TCR alpha chain-TRAV21-TRAJ8, beta chain- TRBV7-8, antigen-presenting glycoprotein…”. X-ray diffraction, 2 ligands (JLS, NAG), 10 pockets (best druggability 0.88). MolNFT v1 #109215 on GenesisL1: 3D…
- PDB
- 4WW2
- Type
- protein
- Length
- 817 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TCR alpha chain-TRAV21-TRAJ8; TCR beta chain-TRBV7-8; Antigen-presenting glycoprotein…
- UniProt
- P15813, P61769
- Ligands
- JLS, NAG
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TCR alpha chain-TRAV21-TRAJ8 | protein | 203 | 1% helix, 47% strand | — |
| B | TCR beta chain-TRBV7-8 | protein | 243 | 7% helix, 49% strand | — |
| C | Antigen-presenting glycoprotein CD1D | protein | 275 | 25% helix, 39% strand | P15813 |
| F | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P61769 |
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, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.88 | 0.93 | 65 | JLS |
| 2 | 1004 | 0.73 | 0.76 | 84 | empty |
| 3 | 475 | 0.68 | 0.79 | 46 | empty |
| 4 | 305 | 0.60 | 0.78 | 39 | empty |
| 5 | 62 | 0.57 | 0.89 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2258 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 1073 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 371 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4WW2 · Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain F against A, TM-score 0.98
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 4WW2 · PDBe 4WW2 · UniProt P15813 · UniProt P61769
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