MolNFT v2 · #114421 · protein
Crystal structure of phosphoribulokinase from Methanospirillum hungatei
5B3F · Phosphoribulokinase/uridine kinase: “Crystal structure of phosphoribulokinase from Methanospirillum hungatei”. X-ray diffraction at 2.5, 1 ligand (SO4), 8 pockets (best druggability 0.68). MolNFT v2 #114421 on GenesisL1: 3D…
- PDB
- 5B3F
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Methanospirillum hungatei JF-1
- Molecule
- Phosphoribulokinase/uridine kinase
- UniProt
- Q2FUB5
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribulokinase/uridine kinase | protein | 306 | 42% helix, 24% strand | Q2FUB5 |
| B | Phosphoribulokinase/uridine kinase | protein | 306 | 41% helix, 24% strand | Q2FUB5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.68 | 0.80 | 52 | SO4 |
| 2 | 55 | 0.63 | 0.93 | 14 | empty |
| 3 | 95 | 0.56 | 0.85 | 19 | empty |
| 4 | 170 | 0.53 | 0.79 | 37 | empty |
| 5 | 138 | 0.47 | 0.78 | 25 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1730 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5B3F · Crystal structure of phosphoribulokinase from methanospirillum hungatei · the same entry in another collection · chain A against A, TM-score 1.00
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 Q2FUB5
- Elsewhere: RCSB PDB 5B3F · PDBe 5B3F · UniProt Q2FUB5
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