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Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with nigerotriose
Analyse Crystal structure of Lactococcus lactis subsp. cremoris GH31… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WJD
- Type
- protein
- Length
- 729 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Lactococcus lactis subsp. cremoris MG1363
- Molecule
- Alpha-xylosidase
- EC
- 3.2.1.-
- UniProt
- A2RM80
- Ligands
- GLC, BGC
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-xylosidase (EC 3.2.1.-) | protein | 729 | 29% helix, 24% strand | A2RM80 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.66 | 0.81 | 37 | empty |
| 2 | 400 | 0.62 | 0.77 | 48 | empty |
| 3 | 225 | 0.51 | 0.76 | 30 | empty |
| 4 | 63 | 0.51 | 0.86 | 19 | GLC |
| 5 | 69 | 0.50 | 0.85 | 15 | empty |
Compared structures
- 7WJD · Crystal structure of lactococcus lactis subsp. cremoris GH31 alpha-1, 3-glucosidase… · 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 A2RM80
- Elsewhere: RCSB PDB 7WJD · PDBe 7WJD · UniProt A2RM80
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