MolNFT v1 · #122831 · protein
Antigen presenting molecule
5J1A · T-cell surface glycoprotein CD1A: “Antigen presenting molecule”. X-ray diffraction, 1 ligand (6F8), 4 pockets (best druggability 0.86). MolNFT v1 #122831 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5J1A
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1A; Beta-2-microglobulin
- UniProt
- P06126, P61769
- Ligands
- 6F8
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A | protein | 270 | 29% helix, 41% strand | P06126 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
Ligands and binding sites
- 6F8 · 3-[(8Z,11Z)-pentadeca-8,11-dien-1-yl]benzene-1,2-diol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.86 | 0.89 | 50 | 6F8 |
| 2 | 348 | 0.63 | 0.79 | 44 | empty |
| 3 | 107 | 0.38 | 0.75 | 24 | empty |
| 4 | 79 | 0.31 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1379 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5J1A · Antigen presenting molecule · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.97
- 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
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 5J1A · PDBe 5J1A · UniProt P06126 · UniProt P61769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.