MolNFT v1 · #147201 · protein
Crystal structure of the apo domain-swapped dimer Q108K:T51D:A28C mutant of human cellular retinol binding protein II
6E5R · Retinol-binding protein 2: “Crystal structure of the apo domain-swapped dimer Q108K:T51D:A28C mutant of human cellular retinol binding…”. X-ray diffraction, 2 pockets (best druggability 0.84). MolNFT v1 #147201 on GenesisL1: 3D…
- PDB
- 6E5R
- 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 0.84
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinol-binding protein 2 | protein | 133 | 11% helix, 58% strand | P50120 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 3 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 | 226 | 0.84 | 0.96 | 34 | GOL |
| 2 | 218 | 0.83 | 0.96 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 4013 Ų buried · 77 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6E5R · Crystal structure of the apo domain-swapped dimer Q108K:T51D:A28C mutant of human… · 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 0.58
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 6E5R · PDBe 6E5R · UniProt P50120
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