Research workbench
Structure of escherichia COLI ribose-5-phosphate isomerase, rpia, complexed with arabinose-5-phosphate.
Analyse Structure of escherichia COLI ribose-5-phosphate isomerase, rpia, complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O8B
- Type
- protein
- Length
- 380 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose 5-phosphate isomerase
- EC
- 5.3.1.6
- UniProt
- P0A7Z0
- Ligands
- ABF
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose 5-phosphate isomerase (EC 5.3.1.6) | protein | 168 | 23% helix, 36% strand | P0A7Z0 |
| B | Ribose 5-phosphate isomerase (EC 5.3.1.6) | protein | 212 | 34% helix, 30% strand | P0A7Z0 |
Ligands and binding sites
- ABF · 5-O-phosphono-beta-D-arabinofuranose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.46 | 0.78 | 21 | empty |
| 2 | 123 | 0.42 | 0.76 | 20 | empty |
| 3 | 68 | 0.36 | 0.78 | 20 | ABF |
| 4 | 52 | 0.33 | 0.78 | 17 | ABF |
| 5 | 54 | 0.31 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1110 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 1O8B · Structure of Escherichia coli ribose-5-phosphate isomerase, RpiA, complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A7Z0 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase a (P0A7Z0) · 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 P0A7Z0
- Elsewhere: RCSB PDB 1O8B · PDBe 1O8B · UniProt P0A7Z0
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