MolNFT v1 · #116824 · protein
Crystal structure of E72A mutant of domain swapped dimer human cellular retinol binding protein
5DPQ · Retinol-binding protein 2: “Crystal structure of E72A mutant of domain swapped dimer human cellular retinol binding protein”. X-ray diffraction, 2 pockets (best druggability 0.81). MolNFT v1 #116824 on GenesisL1: 3D structure…
- PDB
- 5DPQ
- 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
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinol-binding protein 2 | protein | 133 | 11% helix, 59% strand | P50120 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.81 | 0.89 | 51 | ACT |
| 2 | 366 | 0.78 | 0.87 | 48 | ACT |
Interfaces
1 interface between chains.
- A–B · 3908 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 5DPQ · Crystal Structure of E72A mutant of domain swapped dimer Human Cellular Retinol Binding… · 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 0.57
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 5DPQ · PDBe 5DPQ · UniProt P50120
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