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Structure of the D125N mutant of the catalytic domain of the bacillus circulans alpha-1,6 mannanase in complex with an alpha-1,6-alpha- manno-cyclophellitol trisaccharide inhibitor
Analyse Structure of the D125N mutant of the catalytic domain of the bacillus circulans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZBW
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannanase
- UniProt
- Q9Z4P9
- Ligands
- PBW, MAN
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,6-mannanase | protein | 330 | 64% helix, 8% strand | Q9Z4P9 |
| B | Alpha-1,6-mannanase | protein | 335 | 63% helix, 8% strand | Q9Z4P9 |
Ligands and binding sites
- PBW · (1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3, 4,5-pentol · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
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 | 537 | 0.67 | 0.78 | 43 | EDO |
| 2 | 214 | 0.54 | 0.77 | 27 | EDO |
| 3 | 81 | 0.34 | 0.75 | 15 | MAN, PBW |
| 4 | 67 | 0.34 | 0.76 | 13 | MAN, PBW |
| 5 | 76 | 0.31 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 459 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6ZBW · Structure of the D125N mutant of the catalytic domain of the Bacillus circulans alpha-1,6… · 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 Q9Z4P9
- Elsewhere: RCSB PDB 6ZBW · PDBe 6ZBW · UniProt Q9Z4P9
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