Research workbench
Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) E419A variant in complex with serine and glycerol
Analyse Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OIE
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.071
- Source
- Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)
- Molecule
- hydrolase
- UniProt
- K5BDL0
- Ligands
- SER
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.071 · 1 distinct chain · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | hydrolase | protein | 445 | 50% helix, 6% strand | K5BDL0 |
Ligands and binding sites
- SER · Serine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.83 | 0.85 | 81 | empty |
| 2 | 78 | 0.76 | 0.99 | 23 | GOL, SER |
| 3 | 78 | 0.75 | 0.98 | 26 | GOL, SER |
| 4 | 53 | 0.50 | 0.86 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 611 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5OIE · Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh)… · the same entry in another collection · chain A against A, TM-score 1.00
- K5BDL0 · AlphaFold monomer V2.0 prediction for glucosylglycerate hydrolase (K5BDL0) · a predicted model of the same protein · 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 K5BDL0
- Elsewhere: RCSB PDB 5OIE · PDBe 5OIE · UniProt K5BDL0
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