MolNFT v1 · #106289 · protein
Crystal structure of the Q108K:K40L mutant of human cellular retinol binding proteinii in complex with all-trans-retinal after 24 hour incubation at 1.4 ångström resolution
4RUU · Retinol-binding protein 2: “Crystal structure of the Q108K:K40L mutant of human cellular retinol binding proteinii in complex with…”. X-ray diffraction, 1 ligand (RET), 4 pockets (best druggability 0.85). MolNFT v1 #106289 on…
- PDB
- 4RUU
- 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
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinol-binding protein 2 | protein | 133 | 12% 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
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 | 319 | 0.85 | 0.95 | 37 | RET, ACT |
| 2 | 269 | 0.83 | 0.94 | 35 | RET, ACT |
| 3 | 182 | 0.48 | 0.76 | 20 | empty |
| 4 | 55 | 0.35 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 572 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 4RUU · Crystal structure of the Q108K:K40L mutant of human Cellular Retinol Binding ProteinII in… · 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 0.98
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 4RUU · PDBe 4RUU · UniProt P50120
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