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The crystal structure of the D307A mutant of glycoside HYDROLASE (FAMILY 31) from Ruminococcus obeum ATCC 29174 in complex with isomaltose
Analyse The crystal structure of the D307A mutant of glycoside HYDROLASE (FAMILY 31)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MKK
- Type
- protein
- Length
- 1,328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.91
- Source
- Ruminococcus obeum
- Molecule
- alpha-glucosidase GH31 family
- UniProt
- A5ZY13
- Ligands
- BGC, GLC
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · resolution 1.91 · 1 distinct chain · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | alpha-glucosidase GH31 family | protein | 664 | 28% helix, 26% strand | A5ZY13 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains B, A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.87 | 0.88 | 112 | empty |
| 2 | 619 | 0.67 | 0.76 | 70 | BGC, GLC |
| 3 | 564 | 0.66 | 0.77 | 74 | GLC, BGC |
| 4 | 263 | 0.60 | 0.80 | 31 | empty |
| 5 | 249 | 0.58 | 0.79 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2690 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 3MKK · The crystal structure of the D307A mutant of glycoside hydrolase (family 31) from… · the same entry in another collection · 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 A5ZY13
- Elsewhere: RCSB PDB 3MKK · PDBe 3MKK · UniProt A5ZY13
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