Research workbench

Clostridium perfringens alpha-toxin strain NCTC8237 mutant T74I

Analyse Clostridium perfringens alpha-toxin strain NCTC8237 mutant T74I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WY6
Type: protein
Length: 1,084 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospholipase C
EC: 3.1.4.3
UniProt: Q0TV31
Ligands: CD, CA, ZN
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phospholipase C (EC 3.1.4.3)	protein	361	45% helix, 16% strand	Q0TV31
B	Phospholipase C (EC 3.1.4.3)	protein	365	43% helix, 15% strand	Q0TV31
C	Phospholipase C (EC 3.1.4.3)	protein	358	44% helix, 15% strand	Q0TV31

Ligands and binding sites

CD · Cadmium ion · metal · 15 copies · chains A, B, C
CA · Calcium ion · metal · 4 copies · chains A, B, C
ZN · Zinc ion · metal · 3 copies · chains A, B, C
GOL · Glycerol · additive · 2 copies · chains A, B, C

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	988	0.75	0.78	105	CD, CA
2	322	0.54	0.74	35	empty
3	186	0.50	0.77	25	empty
4	150	0.49	0.78	26	empty
5	60	0.40	0.81	15	empty

Interfaces

3 interfaces between chains.

A–B · 359 Å² buried · 1 hydrogen bond · protein-protein
B–C · 225 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 123 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2WY6 · Clostridium perfringens alpha-toxin strain NCTC8237 mutant T74I · the same entry in another collection · chain A against A, TM-score 1.00
Q0TV31 · AlphaFold monomer V2.0 prediction for phospholipase C (Q0TV31) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q0TV31
Elsewhere: RCSB PDB 2WY6 · PDBe 2WY6 · UniProt Q0TV31

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.