Research workbench
Structure of pentavalent phosphorous intermediate of an enzyme catalyzed phosphoryl transfer reaction observed on cocrystallization with glucose 1-phosphate
Analyse Structure of pentavalent phosphorous intermediate of an enzyme catalyzed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O08
- Type
- protein
- Length
- 221 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-phosphoglucomutase
- EC
- 5.4.2.6
- UniProt
- P71447
- Ligands
- G16, MG
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 221 | 48% helix, 12% strand | P71447 |
Ligands and binding sites
- G16 · 1,6-di-O-phosphono-alpha-D-glucopyranose · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.72 | 0.93 | 28 | G16 |
| 2 | 107 | 0.39 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1O08 · Structure of Pentavalent Phosphorous Intermediate of an Enzyme Catalyzed Phosphoryl… · 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 0.98
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 1O08 · PDBe 1O08 · UniProt P71447
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