Research workbench
The catalytic domain, BCGH76, of bacillus circulans AMAN6 in complex with msmsme
Analyse The catalytic domain, BCGH76, of bacillus circulans AMAN6 in complex with msmsme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D4B
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannanase
- EC
- 3.2.1.101
- UniProt
- Q9Z4P9
- Ligands
- MSX, MAN
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,6-mannanase (EC 3.2.1.101) | protein | 333 | 63% helix, 8% strand | Q9Z4P9 |
| B | Alpha-1,6-mannanase (EC 3.2.1.101) | protein | 343 | 60% helix, 8% strand | Q9Z4P9 |
Ligands and binding sites
- MSX · methyl 1,6-dithio-alpha-D-mannopyranoside · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.65 | 0.80 | 34 | empty |
| 2 | 268 | 0.54 | 0.76 | 26 | empty |
| 3 | 238 | 0.52 | 0.76 | 37 | empty |
| 4 | 158 | 0.48 | 0.77 | 21 | empty |
| 5 | 161 | 0.43 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 428 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4D4B · The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with MSMSMe · 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 4D4B · PDBe 4D4B · UniProt Q9Z4P9
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