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Crystal structure of cruzain with nitrile inhibitor N-(2-aminoethyl)- nalpha-benzoyl-L-phenylalaninamide

Analyse Crystal structure of cruzain with nitrile inhibitor N-(2-aminoethyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QH6
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: 33L
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Cruzipain (EC 3.4.22.51)	protein	215	27% helix, 26% strand	P25779

Ligands and binding sites

33L · N-(2-aminoethyl)-Nalpha-benzoyl-L-phenylalaninamide · ligand · chains A

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	952	0.70	0.75	71	empty
2	321	0.64	0.80	28	empty
3	355	0.58	0.76	49	empty
4	70	0.39	0.79	18	33L
5	58	0.34	0.77	18	empty

Interfaces

6 interfaces between chains.

A–B · 711 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 707 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 701 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 467 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 285 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 15 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

4QH6 · Crystal structure of cruzain with nitrile inhibitor… · 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 B 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 4QH6 · PDBe 4QH6 · UniProt P25779

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