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Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region of pasteurella multocida toxin

Analyse Crystal structures reveal a thiol-protease like catalytic triad in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EC5
Type: protein
Length: 1,422 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dermonecrotic toxin
UniProt: P17452
Pockets: 18 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dermonecrotic toxin	protein	711	44% helix, 13% strand	P17452

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	659	0.74	0.80	75	empty
2	54	0.64	0.94	16	empty
3	325	0.63	0.79	35	empty
4	115	0.61	0.86	19	empty
5	77	0.56	0.87	27	empty

Interfaces

1 interface between chains.

A–B · 719 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2EC5 · Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region… · the same entry in another collection · chain A against A, TM-score 1.00
P17452 · AlphaFold monomer V2.0 prediction for dermonecrotic toxin (P17452) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P17452
Elsewhere: RCSB PDB 2EC5 · PDBe 2EC5 · UniProt P17452

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