MolNFT v1 · #129793 · protein
Structure of the RBBP5 beta-propeller domain
5OV3 · Retinoblastoma-binding protein 5: “Structure of the RBBP5 beta-propeller domain”. X-ray diffraction, 9 pockets (best druggability 0.80). MolNFT v1 #129793 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OV3
- Type
- protein
- Length
- 653 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoblastoma-binding protein 5
- UniProt
- Q8BX09
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoblastoma-binding protein 5 | protein | 330 | 2% helix, 48% strand | Q8BX09 |
| B | Retinoblastoma-binding protein 5 | protein | 317 | 3% helix, 50% strand | Q8BX09 |
| C | Retinoblastoma-binding protein 5 | protein | 6 | 0% helix, 50% strand | Q8BX09 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.80 | 0.84 | 60 | empty |
| 2 | 679 | 0.80 | 0.84 | 58 | empty |
| 3 | 71 | 0.49 | 0.84 | 18 | PG4 |
| 4 | 144 | 0.44 | 0.76 | 27 | empty |
| 5 | 91 | 0.42 | 0.78 | 20 | PGE |
Interfaces
3 interfaces between chains.
- A–B · 1873 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 326 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q8BX09
- Elsewhere: RCSB PDB 5OV3 · PDBe 5OV3 · UniProt Q8BX09
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