Research workbench
Catalytic domain of GH87 alpha-1,3-glucanase D1068A in complex with nigerose
Analyse Catalytic domain of GH87 alpha-1,3-glucanase D1068A in complex with nigerose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K0Q
- Type
- protein
- Length
- 559 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.564
- Source
- Paenibacillus glycanilyticus
- Molecule
- Alpha-1,3-glucanase
- UniProt
- A0A068PS59
- Ligands
- GLC, BGC, CA, SO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · resolution 1.564 · 1 distinct chain · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,3-glucanase | protein | 559 | 3% helix, 47% strand | A0A068PS59 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 5 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- ACY · Acetic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.62 | 0.78 | 40 | GLC, ACY |
| 2 | 205 | 0.52 | 0.77 | 22 | BGC, GLC |
| 3 | 157 | 0.42 | 0.74 | 22 | empty |
| 4 | 58 | 0.32 | 0.76 | 15 | empty |
| 5 | 58 | 0.30 | 0.75 | 16 | empty |
Compared structures
- 6K0Q · Catalytic domain of GH87 alpha-1,3-glucanase D1068A in complex with nigerose · 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 A0A068PS59
- Elsewhere: RCSB PDB 6K0Q · PDBe 6K0Q · UniProt A0A068PS59
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