MolNFT v1 · #144595 · protein
Crystal structure of the nucleophile mutant (E575A) of the GH2 exo- beta-mannanase from xanthomonas axonopodis pv. citri
6BYG · Beta-mannosidase: “Crystal structure of the nucleophile mutant (E575A) of the GH2 exo- beta-mannanase from xanthomonas…”. X-ray diffraction, 1 ligand (BMA), 16 pockets (best druggability 0.78). MolNFT v1 #144595 on GenesisL1: 3D…
- PDB
- 6BYG
- Type
- protein
- Length
- 1,714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase
- UniProt
- Q8PI23
- Ligands
- BMA
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannosidase | protein | 856 | 26% helix, 35% strand | Q8PI23 |
| B | Beta-mannosidase | protein | 858 | 26% helix, 34% strand | Q8PI23 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.78 | 0.84 | 53 | empty |
| 2 | 581 | 0.78 | 0.84 | 55 | empty |
| 3 | 101 | 0.75 | 0.96 | 32 | empty |
| 4 | 810 | 0.73 | 0.78 | 92 | empty |
| 5 | 638 | 0.73 | 0.79 | 73 | BMA |
Interfaces
1 interface between chains.
- A–B · 1680 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6BYG · Crystal structure of the nucleophile mutant (E575A) of the GH2 exo-beta-mannanase from… · 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 6BYG · PDBe 6BYG · UniProt Q8PI23
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