MolNFT v1 · #109564 · protein
CD1A ternary complex with endogenous lipids and BK6 TCR
4X6D · T-cell surface glycoprotein CD1A: “CD1A ternary complex with endogenous lipids and BK6 TCR”. X-ray diffraction, 4 ligands (OLA, PAM, NAG), 20 pockets (best druggability 0.86). MolNFT v1 #109564 on GenesisL1: 3D structure, binding…
- PDB
- 4X6D
- Type
- protein
- Length
- 1,521 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
- OLA, PAM, NAG, FUC
- Pockets
- 20 · best druggability 0.86
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 | 267 | 27% helix, 41% strand | P06126 |
| B | Beta-2-microglobulin | protein | 86 | 0% helix, 49% strand | P61769 |
| C | T-cell surface glycoprotein CD1A | protein | 218 | 28% helix, 35% strand | P06126 |
| D | Beta-2-microglobulin | protein | 78 | 0% helix, 53% strand | P61769 |
| E | TCR alpha | protein | 189 | 5% helix, 49% strand | — |
| F | TCR beta | protein | 241 | 7% helix, 51% strand | — |
| G | TCR alpha | protein | 200 | 5% helix, 47% strand | — |
| H | TCR beta | protein | 242 | 7% helix, 51% strand | — |
Ligands and binding sites
- OLA · Oleic acid · ligand · chains A
- PAM · Palmitoleic acid · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.86 | 0.90 | 57 | OLA |
| 2 | 684 | 0.85 | 0.88 | 54 | PAM |
| 3 | 1037 | 0.76 | 0.78 | 94 | empty |
| 4 | 747 | 0.73 | 0.79 | 74 | empty |
| 5 | 613 | 0.70 | 0.78 | 57 | empty |
Interfaces
10 interfaces between chains.
- G–H · 2293 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2133 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1152 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 975 Ų buried · 14 hydrogen bonds · protein-protein
- A–G · 501 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 4X6D · CD1a ternary complex with endogenous lipids 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 0.97
- P06126 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1A (P06126) · a predicted model of the same protein · chain A 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 4X6D · PDBe 4X6D · UniProt P06126 · UniProt P61769
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