Research workbench
R49K variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer to 1.6 A.
Analyse R49K variant of beta-phosphoglucomutase from Lactococcus lactis in an open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HDH
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.62
- Source
- Lactococcus lactis subsp. lactis
- Molecule
- Beta-phosphoglucomutase
- EC
- 5.4.2.6
- UniProt
- P71447
- Ligands
- MG
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.62 · 1 distinct chain · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-phosphoglucomutase (EC 5.4.2.6) | protein | 218 | 52% helix, 11% strand | P71447 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- ACT · Acetate ion · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.71 | 0.78 | 54 | EDO |
| 2 | 662 | 0.68 | 0.77 | 54 | EDO, ACT |
Interfaces
1 interface between chains.
- A–B · 618 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6HDH · R49K variant of beta-phosphoglucomutase from lactococcus lactis in an open conformer to… · 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 0.86
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 6HDH · PDBe 6HDH · UniProt P71447
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