MolNFT v2 · #129900 · protein
5-fluorotryptophan labeled beta-phosphoglucomutase in a closed conformation, monoclinic crystal form
5OLY: “5-fluorotryptophan labeled beta-phosphoglucomutase in a closed conformation, monoclinic crystal form”. X-ray diffraction at 2, 3 ligands (MGF, G6P, MG), 6 pockets (best druggability 0.73). MolNFT v2 #129900 on GenesisL1: 3D…
- PDB
- 5OLY
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Lactococcus lactis subsp. lactis
- Molecule
- Beta-phosphoglucomutase
- EC
- 5.4.2.6
- UniProt
- P71447
- Ligands
- MGF, G6P, MG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 220 | 51% helix, 12% strand | P71447 |
| G | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 221 | 51% helix, 12% strand | P71447 |
Ligands and binding sites
- MGF · Trifluoromagnesate · ligand · 2 copies · chains A, G
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 2 copies · chains A, G
- MG · Magnesium ion · metal · 4 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.73 | 0.91 | 32 | MGF, MG, G6P |
| 2 | 136 | 0.73 | 0.92 | 34 | MG, G6P, MGF |
| 3 | 171 | 0.47 | 0.76 | 23 | empty |
| 4 | 89 | 0.38 | 0.76 | 19 | empty |
| 5 | 94 | 0.36 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–G · 209 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5OLY · 5-fluorotryptophan labeled beta-phosphoglucomutase in a closed conformation, monoclinic… · the same entry in another collection · chain A against A, TM-score 1.00
- P71447 · AlphaFold monomer V2.0 prediction for beta-phosphoglucomutase (P71447) · a predicted model of the same protein · chain G 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 P71447
- Elsewhere: RCSB PDB 5OLY · PDBe 5OLY · UniProt P71447
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