MolNFT v1 · #118579 · protein
Crystal structure of the Q108K:K40L:T51V:R58Y:Y19W mutant of human cellular retinol binding protein II in complex with all-trans-retinal at 1.3 ångström resolution
5F6B · Retinol-binding protein 2: “Crystal structure of the Q108K:K40L:T51V:R58Y:Y19W mutant of human cellular retinol binding protein II in…”. X-ray diffraction, 1 ligand (RET), 5 pockets (best druggability 0.81). MolNFT v1 #118579 on…
- PDB
- 5F6B
- Type
- protein
- Length
- 266 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Ligands
- RET
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinol-binding protein 2 | protein | 133 | 11% helix, 56% strand | P50120 |
Ligands and binding sites
- RET · Retinal · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
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 | 308 | 0.81 | 0.91 | 38 | RET, ACT |
| 2 | 306 | 0.80 | 0.90 | 40 | RET, ACT |
| 3 | 131 | 0.54 | 0.81 | 24 | empty |
| 4 | 53 | 0.31 | 0.76 | 15 | empty |
| 5 | 53 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 618 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 5F6B · Crystal structure of the Q108K:K40L:T51V:R58Y:Y19W mutant of human Cellular Retinol… · the same entry in another collection · chain A against A, TM-score 1.00
- P50120 · AlphaFold monomer V2.0 prediction for retinol-binding protein 2 (P50120) · a predicted model of the same protein · chain A 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 P50120
- Elsewhere: RCSB PDB 5F6B · PDBe 5F6B · UniProt P50120
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