MolNFT v1 · #92900 · protein
Crystal structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius UCC118
4GMK · Ribose-5-phosphate isomerase a: “Crystal structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius UCC118”. X-ray diffraction, 2 ligands (K, PO4), 4 pockets (best druggability 0.46). MolNFT v1…
- PDB
- 4GMK
- Type
- protein
- Length
- 451 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
- Q1WR87
- Ligands
- K, PO4
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 227 | 34% helix, 27% strand | Q1WR87 |
| B | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 224 | 33% helix, 28% strand | Q1WR87 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.46 | 0.77 | 21 | K |
| 2 | 140 | 0.41 | 0.75 | 22 | empty |
| 3 | 93 | 0.37 | 0.76 | 28 | PO4 |
| 4 | 51 | 0.36 | 0.81 | 18 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1182 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4GMK · Crystal Structure of Ribose 5-Phosphate Isomerase from the Probiotic Bacterium… · 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 Q1WR87
- Elsewhere: RCSB PDB 4GMK · PDBe 4GMK · UniProt Q1WR87
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