MolNFT v1 · #144593 · protein
Crystal structure of the GH2 exo-beta-mannanase from xanthomonas axonopodis pv. citri in complex with mannose
6BYE · Beta-mannosidase: “Crystal structure of the GH2 exo-beta-mannanase from xanthomonas axonopodis pv. citri in complex with mannose”. X-ray diffraction, 1 ligand (BMA), 15 pockets (best druggability 0.77). MolNFT v1 #144593 on…
- PDB
- 6BYE
- Type
- protein
- Length
- 1,722 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase
- UniProt
- Q8PI23
- Ligands
- BMA
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-mannosidase | protein | 861 | 26% helix, 34% strand | Q8PI23 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.77 | 0.83 | 53 | empty |
| 2 | 536 | 0.77 | 0.84 | 60 | empty |
| 3 | 100 | 0.76 | 0.96 | 27 | empty |
| 4 | 1176 | 0.76 | 0.79 | 126 | empty |
| 5 | 591 | 0.72 | 0.80 | 69 | BMA, ACT |
Interfaces
1 interface between chains.
- A–B · 1638 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 6BYE · Crystal structure of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri in… · 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 Q8PI23
- Elsewhere: RCSB PDB 6BYE · PDBe 6BYE · UniProt Q8PI23
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