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Crystal structure analysis of cruzain bound to vinyl sulfone analog of wrr-483 (wrr-666)
Analyse Crystal structure analysis of cruzain bound to vinyl sulfone analog of wrr-483… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PI3
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cruzipain
- EC
- 3.4.22.51
- UniProt
- P25779
- Ligands
- 2V5
- 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, B | Cruzipain (EC 3.4.22.51) | protein | 215 | 25% helix, 23% strand | P25779 |
Ligands and binding sites
- 2V5 · N-[(2S)-5-(carbamimidamidooxy)-1-oxo-1-{[(1E,3S)-5-phenyl-1-(phenylsulfonyl)pent-1-en-3-yl]amino}pentan-2-yl]-4-methylpiperazine-1-carboxamide · ligand · 2 copies · chains A, B
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 | 850 | 0.73 | 0.77 | 52 | 2V5 |
| 2 | 65 | 0.44 | 0.83 | 19 | empty |
| 3 | 68 | 0.42 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 641 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 4PI3 · Crystal structure analysis of cruzain bound to vinyl sulfone analog of WRR-483 (WRR-666) · 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 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 P25779
- Elsewhere: RCSB PDB 4PI3 · PDBe 4PI3 · UniProt P25779
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