Research workbench
Crystal structure analysis of cruzain bound to vinyl sulfone derived inhibitor (WRR483)
Analyse Crystal structure analysis of cruzain bound to vinyl sulfone derived inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LXS
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cruzain
- EC
- 3.4.22.51
- UniProt
- P25779
- Ligands
- 4MC, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cruzain (EC 3.4.22.51) | protein | 215 | 25% helix, 23% strand | P25779 |
Ligands and binding sites
- 4MC · (Z)-N-(5-guanidino-1-oxo-1-(5-phenyl-1-(phenylsulfonyl)pent-1-en-3-ylamino)pentan-2-yl)-4-methylpiperazine-1-carboxamid E · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, C
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 | 888 | 0.73 | 0.77 | 54 | 4MC, EDO |
| 2 | 71 | 0.46 | 0.82 | 19 | empty |
| 3 | 64 | 0.41 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 635 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3LXS · Crystal structure analysis of cruzain bound to vinyl sulfone derived inhibitor (WRR483) · the same entry in another collection · chain A against A, TM-score 1.00
- P25779 · AlphaFold monomer V2.0 prediction for cruzipain (P25779) · a predicted model of the same protein · chain C 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 P25779
- Elsewhere: RCSB PDB 3LXS · PDBe 3LXS · UniProt P25779
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