MolNFT v1 · #127566 · protein
The catalytic domain, BCGH76, of bacillus circulans AMAN6 in complex with 1,6-mansifg
5N0F · Alpha-1,6-mannanase: “The catalytic domain, BCGH76, of bacillus circulans AMAN6 in complex with 1,6-mansifg”. X-ray diffraction, 1 ligand (7K2), 7 pockets (best druggability 0.66). MolNFT v1 #127566 on GenesisL1: 3D structure…
- PDB
- 5N0F
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannanase
- UniProt
- Q9Z4P9
- Ligands
- 7K2
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,6-mannanase | protein | 332 | 63% helix, 8% strand | Q9Z4P9 |
| B | Alpha-1,6-mannanase | protein | 342 | 61% helix, 8% strand | Q9Z4P9 |
Ligands and binding sites
- 7K2 · [(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannopyranoside · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.66 | 0.80 | 38 | empty |
| 2 | 279 | 0.58 | 0.78 | 29 | empty |
| 3 | 260 | 0.54 | 0.76 | 23 | empty |
| 4 | 247 | 0.54 | 0.76 | 27 | empty |
| 5 | 143 | 0.42 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 456 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5N0F · The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManSIFG · 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 5N0F · PDBe 5N0F · UniProt Q9Z4P9
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