Research workbench
CD1A ternary complex with lysophosphatidylcholine and BK6 TCR
Analyse CD1A ternary complex with lysophosphatidylcholine and BK6 TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X6C
- Type
- protein
- Length
- 1,585 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1A; Beta-2-microglobulin; TCR alpha; TCR beta
- UniProt
- P06126, P61769
- Ligands
- 42H, NAG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A | protein | 263 | 26% helix, 38% strand | P06126 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C | T-cell surface glycoprotein CD1A | protein | 249 | 27% helix, 42% strand | P06126 |
| D | Beta-2-microglobulin | protein | 90 | 0% helix, 47% strand | P61769 |
| E | TCR alpha | protein | 198 | 3% helix, 46% strand | — |
| F | TCR beta | protein | 243 | 7% helix, 49% strand | — |
| G | TCR alpha | protein | 201 | 3% helix, 48% strand | — |
| H | TCR beta | protein | 243 | 7% helix, 51% strand | — |
Ligands and binding sites
- 42H · (4R,7R,18Z)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, G, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.85 | 0.90 | 50 | 42H |
| 2 | 600 | 0.84 | 0.88 | 51 | 42H |
| 3 | 1155 | 0.76 | 0.79 | 106 | empty |
| 4 | 889 | 0.73 | 0.78 | 99 | empty |
| 5 | 546 | 0.69 | 0.78 | 52 | empty |
Interfaces
11 interfaces between chains.
- G–H · 2245 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2182 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1224 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1213 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 513 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4X6C · CD1a ternary complex with lysophosphatidylcholine and BK6 TCR · the same entry in another collection · chain H against H, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P06126 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1A (P06126) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P06126
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4X6C · PDBe 4X6C · UniProt P06126 · UniProt P61769
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