Research workbench
Crystal structure of ribose-5-isomerase a from francisella tularensis
Analyse Crystal structure of ribose-5-isomerase a from francisella tularensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IO1
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-5-phosphate isomerase a
- EC
- 5.3.1.6
- UniProt
- Q5NFM5
- Ligands
- CL, PO4, BR
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 218 | 34% helix, 27% strand | Q5NFM5 |
| B | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 215 | 35% helix, 29% strand | Q5NFM5 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.53 | 0.83 | 25 | empty |
| 2 | 106 | 0.47 | 0.79 | 22 | empty |
| 3 | 55 | 0.39 | 0.81 | 18 | CL, PO4 |
| 4 | 61 | 0.36 | 0.78 | 19 | empty |
| 5 | 60 | 0.35 | 0.78 | 16 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1312 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4IO1 · Crystal structure of ribose-5-isomerase A from Francisella Tularensis · the same entry in another collection · chain A against A, TM-score 1.00
- Q5NFM5 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase a (Q5NFM5) · 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 Q5NFM5
- Elsewhere: RCSB PDB 4IO1 · PDBe 4IO1 · UniProt Q5NFM5
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