Research workbench
Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase(MhGgH) E419A variant in complex with glucosylglycerol
Analyse Crystal structure of Mycolicibacterium hassiacum glucosylglycerate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ONT
- Type
- protein
- Length
- 877 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)
- Molecule
- Uncharacterized protein
- UniProt
- K5BDL0
- Ligands
- A0K
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.05 · 2 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 440 | 51% helix, 6% strand | K5BDL0 |
| B | Uncharacterized protein | protein | 437 | 51% helix, 6% strand | K5BDL0 |
Ligands and binding sites
- A0K · 1,3-dihydroxypropan-2-yl alpha-D-glucopyranoside · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.81 | 0.85 | 63 | empty |
| 2 | 258 | 0.77 | 0.90 | 34 | A0K |
| 3 | 281 | 0.71 | 0.85 | 37 | empty |
| 4 | 184 | 0.67 | 0.86 | 33 | A0K |
| 5 | 62 | 0.52 | 0.86 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 616 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5ONT · Crystal structure of mycolicibacterium hassiacum glucosylglycerate HYDROLASE(MHGGH) E419A… · 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 B 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 5ONT · PDBe 5ONT · UniProt K5BDL0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.