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Crystal structure of the progenitor M complex of clostridium botulinum type E neurotoxin

Analyse Crystal structure of the progenitor M complex of clostridium botulinum type E… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZKT
Type: protein
Length: 7,047 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bontoxilysin a; Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, ntnh
EC: 3.4.24.69
UniProt: B2V3U7, B2V3U8
Ligands: ZN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Bontoxilysin a (EC 3.4.24.69)	protein	1235	28% helix, 24% strand	B2V3U7
B, D, F	Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, ntnh	protein	1114	32% helix, 20% strand	B2V3U8

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A, C, E

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1010	0.85	0.86	97	empty
2	987	0.85	0.85	97	empty
3	994	0.84	0.85	100	empty
4	906	0.84	0.85	91	empty
5	728	0.83	0.87	79	empty

Interfaces

8 interfaces between chains.

E–F · 3900 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 3800 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 3758 Å² buried · 28 hydrogen bonds · protein-protein
C–E · 577 Å² buried · 7 hydrogen bonds · protein-protein
E–D · 428 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4ZKT · Crystal structure of the progenitor M complex of Clostridium botulinum type E neurotoxin · 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 B2V3U7
Every structure of UniProt B2V3U8
Elsewhere: RCSB PDB 4ZKT · PDBe 4ZKT · UniProt B2V3U7 · UniProt B2V3U8

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