MolNFT v1 · #58826 · protein
Crystal structure of putative ribokinase (10640157) from thermoplasma acidophilum at 1.91 a resolution
3BF5 · Ribokinase related protein: “Crystal structure of putative ribokinase (10640157) from thermoplasma acidophilum at 1.91 a resolution”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.68). MolNFT v1 #58826 on…
- PDB
- 3BF5
- Type
- protein
- Length
- 563 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase related protein
- UniProt
- Q9HJT3
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase related protein | protein | 284 | 38% helix, 28% strand | Q9HJT3 |
| B | Ribokinase related protein | protein | 279 | 37% helix, 28% strand | Q9HJT3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.68 | 0.79 | 35 | PGO |
| 2 | 529 | 0.66 | 0.78 | 51 | PGO |
| 3 | 439 | 0.63 | 0.77 | 49 | empty |
| 4 | 100 | 0.41 | 0.77 | 17 | empty |
| 5 | 97 | 0.41 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 3BF5 · Crystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HJT3 · AlphaFold monomer V2.0 prediction for nucleoside kinase (Q9HJT3) · a predicted model of the same protein · chain B 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 Q9HJT3
- Elsewhere: RCSB PDB 3BF5 · PDBe 3BF5 · UniProt Q9HJT3
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