Research workbench
Crystal structure of cucumisin, a subtilisin-like endoprotease from cucumis melo L
Analyse Crystal structure of cucumisin, a subtilisin-like endoprotease from cucumis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VTA
- Type
- protein
- Length
- 1,185 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
- DFP, NAG, FUC, BMA, MAN
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cucumisin (EC 3.4.21.25) | protein | 591 | 20% helix, 29% strand | Q39547 |
| B | Cucumisin (EC 3.4.21.25) | protein | 594 | 18% helix, 26% strand | Q39547 |
Ligands and binding sites
- DFP · Diisopropyl phosphonate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.86 | 0.87 | 135 | empty |
| 2 | 307 | 0.53 | 0.75 | 47 | DFP |
| 3 | 275 | 0.49 | 0.73 | 44 | DFP |
| 4 | 142 | 0.47 | 0.77 | 19 | empty |
| 5 | 63 | 0.47 | 0.84 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1257 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 3VTA · Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L · the same entry in another collection · chain A against A, TM-score 1.00
- Q39547 · AlphaFold monomer V2.0 prediction for cucumisin (Q39547) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 3VTA · PDBe 3VTA · UniProt Q39547
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