Research workbench
The catalytic domain, BCGH76, of bacillus circulans AMAN6 in complex with 1,6-mandmj
Analyse The catalytic domain, BCGH76, of bacillus circulans AMAN6 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
- 4D4C
- Type
- protein
- Length
- 671 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
- DMJ, 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 | 332 | 64% helix, 8% strand | Q9Z4P9 |
| B | Alpha-1,6-mannanase (EC 3.2.1.101) | protein | 339 | 60% helix, 8% strand | Q9Z4P9 |
Ligands and binding sites
- DMJ · 1-deoxymannojirimycin · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
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 | 323 | 0.65 | 0.80 | 29 | empty |
| 2 | 289 | 0.57 | 0.77 | 29 | empty |
| 3 | 223 | 0.53 | 0.77 | 30 | empty |
| 4 | 166 | 0.46 | 0.76 | 18 | empty |
| 5 | 149 | 0.41 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 421 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4D4C · The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManDMJ · 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 4D4C · PDBe 4D4C · UniProt Q9Z4P9
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