Research workbench
Crystal structure of mycolicibacterium hassiacum glucosylglycerate hydrolase (mhggh) D182A variant in complex with glucosylglycerate
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
- 5OIW
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- K5BDL0
- Ligands
- 9WN
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 445 | 51% helix, 6% strand | K5BDL0 |
Ligands and binding sites
- 9WN · (2R)-2-(alpha-D-glucopyranosyloxy)-3-hydroxypropanoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 12 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PGE · Triethylene glycol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.83 | 0.85 | 89 | GOL |
| 2 | 85 | 0.78 | 0.99 | 23 | 9WN |
| 3 | 74 | 0.76 | 0.98 | 20 | 9WN |
| 4 | 72 | 0.55 | 0.86 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 610 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5OIW · 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 5OIW · PDBe 5OIW · UniProt K5BDL0
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