Research workbench
Crystal structure of human TCR alpha chain-TRAV12-3, beta chain-TRBV6- 5, antigen-presenting molecule CD1D, and beta-2-microglobulin
Analyse Crystal structure of human TCR alpha chain-TRAV12-3, beta chain-TRBV6- 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WWK
- Type
- protein
- Length
- 797 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TCR alpha chain-TRAV12-3; TCR beta chain-TRBV6-5; Antigen-presenting glycoprotein CD1D…
- UniProt
- P15813, P61769
- Ligands
- JLS, NAG
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TCR alpha chain-TRAV12-3 | protein | 188 | 5% helix, 37% strand | — |
| B | TCR beta chain-TRBV6-5 | protein | 240 | 7% helix, 49% strand | — |
| C | Antigen-presenting glycoprotein CD1D | protein | 270 | 26% helix, 39% strand | P15813 |
| D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% 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 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
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.86 | 0.90 | 65 | JLS |
| 2 | 439 | 0.69 | 0.81 | 70 | empty |
| 3 | 471 | 0.65 | 0.77 | 48 | empty |
| 4 | 363 | 0.63 | 0.78 | 43 | empty |
| 5 | 357 | 0.62 | 0.78 | 59 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1330 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1316 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 508 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 299 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4WWK · Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-TRBV6-5… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D 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 4WWK · PDBe 4WWK · UniProt P15813 · UniProt P61769
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