Research workbench
Crystal structure of bacillus circulans tn-31 AMAN6 in complex with mannobiose
Analyse Crystal structure of bacillus circulans tn-31 AMAN6 in complex with mannobiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BOJ
- Type
- protein
- Length
- 1,010 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannanase
- UniProt
- Q9Z4P9
- Ligands
- MAN
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,6-mannanase | protein | 336 | 62% helix, 8% strand | Q9Z4P9 |
| B | Alpha-1,6-mannanase | protein | 330 | 63% helix, 8% strand | Q9Z4P9 |
| C | Alpha-1,6-mannanase | protein | 344 | 61% helix, 8% strand | Q9Z4P9 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.81 | 0.83 | 89 | MAN |
| 2 | 716 | 0.68 | 0.76 | 59 | empty |
| 3 | 313 | 0.60 | 0.78 | 34 | empty |
| 4 | 260 | 0.56 | 0.77 | 27 | empty |
| 5 | 141 | 0.42 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 660 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 348 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 326 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4BOJ · Crystal structure of Bacillus circulans TN-31 Aman6 in complex with mannobiose · 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 4BOJ · PDBe 4BOJ · UniProt Q9Z4P9
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