MolNFT v1 · #116564 · protein

Crystal structure of toxin, mutant N197W

5DHL · Perfringolysin O: “Crystal structure of toxin, mutant N197W”. X-ray diffraction, 13 pockets (best druggability 0.83). MolNFT v1 #116564 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DHL
Type: protein
Length: 934 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Perfringolysin O
UniProt: P0C2E9
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Perfringolysin O	protein	467	20% helix, 41% strand	P0C2E9

Ligands and binding sites

EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	941	0.83	0.84	107	empty
2	887	0.83	0.85	106	EPE
3	163	0.62	0.84	25	empty
4	175	0.61	0.83	24	empty
5	384	0.57	0.75	27	empty

Interfaces

1 interface between chains.

A–B · 1828 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

P0C2E9 · AlphaFold monomer V2.0 prediction for perfringolysin O (P0C2E9) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P0C2E9
Elsewhere: RCSB PDB 5DHL · PDBe 5DHL · UniProt P0C2E9

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