MolNFT v1 · #21127 · protein

Crystal structure of botulinum neurotoxin type B at pH 5.5

1S0D: “Crystal structure of botulinum neurotoxin type B at pH 5.5”. X-ray diffraction, 2 ligands (CA, ZN), 13 pockets (best druggability 0.84). MolNFT v1 #21127 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1S0D
Type: protein
Length: 1,287 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Botulinum neurotoxin type B
EC: 3.4.24.69
UniProt: P10844
Ligands: CA, ZN
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Botulinum neurotoxin type B (EC 3.4.24.69)	protein	1287	32% helix, 23% strand	P10844

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A
ZN · Zinc ion · metal · chains A

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

Pockets

13 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	1070	0.84	0.85	108	ZN
2	457	0.77	0.85	67	empty
3	278	0.63	0.80	30	empty
4	83	0.61	0.89	23	empty
5	253	0.57	0.78	36	empty

Compared structures

1S0D · Crystal structure of botulinum neurotoxin type B at pH 5.5 · the same entry in another collection · chain A against A, TM-score 1.00
P10844 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type B (P10844) · a predicted model of the same protein · chain A against A, TM-score 0.67

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 P10844
Elsewhere: RCSB PDB 1S0D · PDBe 1S0D · UniProt P10844

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