Research workbench

R32 closed form of alpha-toxin from clostridium perfringens strain CER89L43

Analyse R32 closed form of alpha-toxin from clostridium perfringens strain CER89L43 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GYG
Type: protein
Length: 740 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospholipase C
EC: 3.1.4.3
UniProt: P15310
Ligands: ZN
Pockets: 8 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phospholipase C (EC 3.1.4.3)	protein	370	43% helix, 16% strand	P15310

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	240	0.68	0.85	40	empty
2	179	0.66	0.86	33	empty
3	295	0.62	0.80	46	empty
4	168	0.62	0.84	33	empty
5	102	0.40	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 256 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1GYG · R32 closed form of alpha-toxin from clostridium perfringens strain CER89L43 · the same entry in another collection · chain A against A, TM-score 1.00

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 P15310
Elsewhere: RCSB PDB 1GYG · PDBe 1GYG · UniProt P15310

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