Research workbench
Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with glucosylglycolate
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
- 5ONZ
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.93
- Source
- Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)
- Molecule
- Hydrolase
- UniProt
- K5BDL0
- Ligands
- SER, 9YW
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.93 · 1 distinct chain · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hydrolase | protein | 445 | 51% helix, 6% strand | K5BDL0 |
Ligands and binding sites
- SER · Serine · ligand · 2 copies · chains A, B
- 9YW · (alpha-D-glucopyranosyloxy)acetic acid · sugar · 3 copies · chains A, B
- GOL · Glycerol · additive · 15 copies · chains A, B
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 | 969 | 0.84 | 0.85 | 84 | GOL |
| 2 | 86 | 0.78 | 0.99 | 23 | GOL, 9YW, SER |
| 3 | 80 | 0.76 | 0.98 | 21 | GOL, 9YW, SER |
| 4 | 50 | 0.50 | 0.87 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 617 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5ONZ · 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 5ONZ · PDBe 5ONZ · UniProt K5BDL0
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