MolNFT v1 · #29308 · protein
Structure of beta-phosphoglucomutase with inhibitor bound alpha- galactose 1-phosphate
1Z4O: “Structure of beta-phosphoglucomutase with inhibitor bound alpha- galactose 1-phosphate”. X-ray diffraction, 2 ligands (GL1, MG), 5 pockets (best druggability 0.74). MolNFT v1 #29308 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1Z4O
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-phosphoglucomutase
- EC
- 5.4.2.6
- UniProt
- P71447
- Ligands
- GL1, MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 219 | 51% helix, 12% strand | P71447 |
| B | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 215 | 49% helix, 12% strand | P71447 |
Ligands and binding sites
- GL1 · 1-O-phosphono-alpha-D-galactopyranose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.74 | 0.96 | 25 | GL1 |
| 2 | 188 | 0.71 | 0.89 | 39 | GL1 |
| 3 | 110 | 0.39 | 0.75 | 19 | empty |
| 4 | 86 | 0.33 | 0.74 | 17 | empty |
| 5 | 50 | 0.25 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 209 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Z4O · Structure of beta-phosphoglucomutase with inhibitor bound alpha-galactose 1-phosphate · 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 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 P71447
- Elsewhere: RCSB PDB 1Z4O · PDBe 1Z4O · UniProt P71447
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