Research workbench
Crystal structure of 9C2 TCR bound to CD1D
Analyse Crystal structure of 9C2 TCR bound to CD1D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LHU
- Type
- protein
- Length
- 801 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D; Beta-2-microglobulin; 9C2 TCR delta chain; 9C2 TCR…
- UniProt
- P15813, P61769
- Ligands
- JLS, NAG, BMA, MG, CL
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D | protein | 272 | 26% helix, 36% strand | P15813 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 47% strand | P61769 |
| D | 9C2 TCR delta chain | protein | 202 | 1% helix, 36% strand | — |
| G | 9C2 TCR gamma chain | protein | 227 | 5% helix, 44% 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, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, D, G
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.85 | 0.87 | 98 | JLS |
| 2 | 189 | 0.64 | 0.84 | 42 | empty |
| 3 | 322 | 0.61 | 0.78 | 41 | empty |
| 4 | 476 | 0.59 | 0.74 | 58 | empty |
| 5 | 134 | 0.49 | 0.79 | 25 | empty |
Interfaces
4 interfaces between chains.
- D–G · 1947 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1359 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 736 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 289 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 4LHU · Crystal Structure of 9C2 TCR bound to CD1d · 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 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 0.97
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 4LHU · PDBe 4LHU · UniProt P15813 · UniProt P61769
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