MolNFT v1 · #88471 · protein
Structure of fungal beta-mannosidase from glycoside hydrolase family 2 of trichoderma harzianum
4CVU: “Structure of fungal beta-mannosidase from glycoside hydrolase family 2 of trichoderma harzianum”. X-ray diffraction, 7 ligands (MAN, NAG, BMA), 9 pockets (best druggability 0.81). MolNFT v1 #88471 on GenesisL1: 3D structure, binding…
- PDB
- 4CVU
- Type
- protein
- Length
- 913 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase
- Ligands
- MAN, NAG, BMA, CD, NA, CA, CL
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannosidase | protein | 913 | 25% helix, 31% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A
- CD · Cadmium ion · metal · 17 copies · chains A
- NA · Sodium ion · metal · 6 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.81 | 0.96 | 19 | empty |
| 2 | 86 | 0.66 | 0.92 | 24 | CD |
| 3 | 238 | 0.56 | 0.78 | 28 | empty |
| 4 | 223 | 0.55 | 0.78 | 32 | CD |
| 5 | 142 | 0.55 | 0.82 | 32 | empty |
Modifications
Observed in the structure: 10 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 4CVU · Structure of Fungal beta-mannosidase from Glycoside Hydrolase Family 2 of Trichoderma… · 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
- Elsewhere: RCSB PDB 4CVU · PDBe 4CVU
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