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Cruzain bound to gallinamide inhibitor

Analyse Cruzain bound to gallinamide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JUJ
Type: protein
Length: 1,290 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cruzipain
EC: 3.4.22.51
UniProt: P25779
Ligands: GN9, K
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Cruzipain (EC 3.4.22.51)	protein	215	26% helix, 25% strand	P25779

Ligands and binding sites

GN9 · gallinamide A, bound form · ligand · 6 copies · chains A, C, B, F, D, E
K · Potassium ion · metal · 14 copies · chains A, B, C, D, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1115	0.78	0.80	123	empty
2	967	0.74	0.77	80	K
3	344	0.59	0.77	58	GN9
4	413	0.58	0.75	35	empty
5	91	0.45	0.80	25	empty

Interfaces

9 interfaces between chains.

D–E · 670 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 633 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 632 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 466 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 442 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 6 covalent (disulfide, covalent ligand).

Compared structures

7JUJ · Cruzain bound to Gallinamide inhibitor · the same entry in another collection · chain F against F, 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 7JUJ · PDBe 7JUJ · UniProt P25779

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