MolNFT v1 · #116516 · protein
Crystal structure of monomer human cellular retinol binding protein II-Y60L
5DG4 · Retinol-binding protein 2: “Crystal structure of monomer human cellular retinol binding protein II-Y60L”. X-ray diffraction, 9 pockets (best druggability 0.81). MolNFT v1 #116516 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5DG4
- Type
- protein
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Retinol-binding protein 2 | protein | 133 | 11% helix, 57% strand | P50120 |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.81 | 0.90 | 41 | ACT |
| 2 | 344 | 0.80 | 0.90 | 39 | empty |
| 3 | 180 | 0.80 | 0.95 | 38 | ACT |
| 4 | 160 | 0.79 | 0.95 | 31 | empty |
| 5 | 262 | 0.56 | 0.77 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–D · 626 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 617 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 433 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DG4 · Crystal structure of monomer human cellular retinol binding protein II-Y60L · 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 0.99
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 5DG4 · PDBe 5DG4 · UniProt P50120
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