MolNFT v1 · #147231 · protein
Crystal structure of human cellular retinol-binding protein 1 in complex with cannabidiorcin (cbdo)
6E6M: “Crystal structure of human cellular retinol-binding protein 1 in complex with cannabidiorcin (cbdo)”. X-ray diffraction, 1 ligand (8CB), 5 pockets (best druggability 0.85). MolNFT v1 #147231 on GenesisL1: 3D structure, binding sites…
- PDB
- 6E6M
- Type
- protein
- Length
- 406 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 1
- UniProt
- P09455
- Ligands
- 8CB
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinol-binding protein 1 | protein | 136 | 12% helix, 55% strand | P09455 |
| B, C | Retinol-binding protein 1 | protein | 135 | 12% helix, 56% strand | P09455 |
Ligands and binding sites
- 8CB · (1'R,2'R)-4,5'-dimethyl-2'-(prop-1-en-2-yl)-1',2',3', 4'-tetrahydro[1,1'-biphenyl]-2,6-diol · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.85 | 0.96 | 35 | 8CB |
| 2 | 277 | 0.84 | 0.95 | 36 | 8CB |
| 3 | 373 | 0.82 | 0.91 | 56 | 8CB |
| 4 | 104 | 0.35 | 0.74 | 16 | empty |
| 5 | 58 | 0.30 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 506 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 441 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 40 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6E6M · Crystal structure of human cellular retinol-binding protein 1 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P09455 · AlphaFold monomer V2.0 prediction for retinol-binding protein 1 (P09455) · 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 P09455
- Elsewhere: RCSB PDB 6E6M · PDBe 6E6M · UniProt P09455
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