Research workbench
Catalytic domain of GH87 alpha-1,3-glucanase D1069A in complex with tetrasaccharides
Analyse Catalytic domain of GH87 alpha-1,3-glucanase D1069A in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K0V
- Type
- protein
- Length
- 2,248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,3-glucanase
- UniProt
- A0A068PS59
- Ligands
- GLC, BGC, CA, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-1,3-glucanase | protein | 562 | 3% helix, 47% strand | A0A068PS59 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 19 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · chains B
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 23 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.80 | 0.84 | 50 | empty |
| 2 | 668 | 0.79 | 0.83 | 49 | empty |
| 3 | 785 | 0.74 | 0.79 | 70 | GLC, SO4 |
| 4 | 343 | 0.64 | 0.79 | 45 | BGC, GLC |
| 5 | 333 | 0.63 | 0.79 | 44 | GLC |
Interfaces
3 interfaces between chains.
- A–C · 1221 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 601 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 368 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6K0V · Catalytic domain of GH87 alpha-1,3-glucanase D1069A in complex with tetrasaccharides · 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 6K0V · PDBe 6K0V · UniProt A0A068PS59
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