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Crystal structure analysis of cruzain with fragment 1 (N-(1H- benzimidazol-2-yl)-1,3-dimethyl-pyrazole-4-carboxamide)

Analyse Crystal structure analysis of cruzain with fragment 1 (N-(1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4W5B
Type: protein
Length: 645 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cruzipain
EC: 3.4.22.51
UniProt: P25779
Ligands: 3H5
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Cruzipain (EC 3.4.22.51)	protein	215	24% helix, 24% strand	P25779

Ligands and binding sites

3H5 · N-(1H-benzimidazol-2-yl)-1,3-dimethyl-1H-pyrazole-4-carboxamide · ligand · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	497	0.56	0.73	61	empty
2	78	0.50	0.84	18	empty
3	77	0.36	0.77	24	3H5
4	56	0.34	0.78	15	3H5
5	56	0.33	0.77	17	3H5

Interfaces

3 interfaces between chains.

A–C · 342 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 219 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 33 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

4W5B · Crystal structure analysis of cruzain with Fragment 1… · 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 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 4W5B · PDBe 4W5B · UniProt P25779

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