MolNFT v1 · #111310 · protein
Crystal structure of cucumisin complex with pro-peptide
4YN3: “Crystal structure of cucumisin complex with pro-peptide”. X-ray diffraction, 5 ligands (NAG, FUC, BMA), 3 pockets (best druggability 0.54). MolNFT v1 #111310 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YN3
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cucumisin
- EC
- 3.4.21.25
- UniProt
- Q39547
- Ligands
- NAG, FUC, BMA, MAN, CL
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cucumisin (EC 3.4.21.25) | protein | 596 | 19% helix, 30% strand | Q39547 |
| B | Cucumisin (EC 3.4.21.25) | protein | 65 | 18% helix, 46% strand | Q39547 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.54 | 0.75 | 37 | PEG |
| 2 | 101 | 0.42 | 0.77 | 18 | empty |
| 3 | 65 | 0.35 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1479 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 Q39547
- Elsewhere: RCSB PDB 4YN3 · PDBe 4YN3 · UniProt Q39547
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