MolNFT v1 · #62718 · protein
Substrate and inhibitor complexes of ribose 5-phosphate isomerase from vibrio vulnificus YJ016
3ENV · Ribose-5-phosphate isomerase a: “Substrate and inhibitor complexes of ribose 5-phosphate isomerase from vibrio vulnificus YJ016”. X-ray diffraction, 1 ligand (ABF), 6 pockets (best druggability 0.43). MolNFT v1 #62718 on GenesisL1…
- PDB
- 3ENV
- Type
- protein
- Length
- 434 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
- Q7MHL9
- Ligands
- ABF
- Pockets
- 6 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 217 | 32% helix, 26% strand | Q7MHL9 |
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
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.43 | 0.80 | 20 | ABF |
| 2 | 98 | 0.42 | 0.78 | 22 | empty |
| 3 | 84 | 0.40 | 0.78 | 21 | empty |
| 4 | 95 | 0.39 | 0.76 | 24 | empty |
| 5 | 70 | 0.39 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1199 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3ENV · Substrate and inhibitor complexes of ribose 5-phosphate isomerase from Vibrio vulnificus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7MHL9 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase a (Q7MHL9) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q7MHL9
- Elsewhere: RCSB PDB 3ENV · PDBe 3ENV · UniProt Q7MHL9
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