Research workbench
Crystal structure of cruzain in complex with the non-covalent inhibitor NEQUIMED176
Analyse Crystal structure of cruzain in complex with the non-covalent inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KLB
- Type
- protein
- Length
- 1,075 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cruzipain
- EC
- 3.4.22.51
- UniProt
- P25779
- Ligands
- 1RV
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cruzipain (EC 3.4.22.51) | protein | 215 | 24% helix, 26% strand | P25779 |
Ligands and binding sites
- 1RV · 2-{[(1H-1,2,4-triazol-5-ylsulfanyl)acetyl]amino}thiophene-3-carboxamide · ligand · 3 copies · chains A, B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.74 | 0.77 | 95 | empty |
| 2 | 439 | 0.62 | 0.76 | 32 | empty |
| 3 | 338 | 0.58 | 0.76 | 43 | empty |
| 4 | 176 | 0.44 | 0.74 | 39 | empty |
| 5 | 50 | 0.23 | 0.72 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 695 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 690 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 679 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 511 Ų buried · 1 hydrogen bond · protein-protein
- B–E · 294 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 4KLB · Crystal Structure of Cruzain in complex with the non-covalent inhibitor Nequimed176 · the same entry in another collection · chain E against E, TM-score 1.00
- P25779 · AlphaFold monomer V2.0 prediction for cruzipain (P25779) · a predicted model of the same protein · chain E 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 4KLB · PDBe 4KLB · UniProt P25779
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