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Binding domain of botulinum neurotoxin dc in complex with human synaptotagmin I

Analyse Binding domain of botulinum neurotoxin dc in complex with human synaptotagmin I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ISQ
Type: protein
Length: 1,286 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neurotoxin; Synaptotagmin-1
UniProt: Q9LBR1, P21579
Ligands: SO4
Pockets: 14 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Neurotoxin	protein	414	7% helix, 49% strand	Q9LBR1
B	Neurotoxin	protein	413	8% helix, 49% strand	Q9LBR1
D, E, F	Synaptotagmin-1	protein	15	73% helix, 0% strand	P21579

Ligands and binding sites

SO4 · Sulfate ion · ion · 20 copies · chains A, F, B, E, C, D
GOL · Glycerol · additive · 8 copies · chains A, B, C

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	338	0.62	0.78	45	GOL
2	230	0.57	0.79	38	empty
3	196	0.56	0.79	35	GOL
4	137	0.53	0.80	24	empty
5	106	0.51	0.82	27	GOL

Interfaces

6 interfaces between chains.

A–C · 924 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 848 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 716 Å² buried · 9 hydrogen bonds · protein-protein
A–F · 702 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 670 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4ISQ · Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I · the same entry in another collection · chain C against C, TM-score 1.00
P21579 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21579) · a predicted model of the same protein · chain D against A, TM-score 0.63

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 Q9LBR1
Every structure of UniProt P21579
Elsewhere: RCSB PDB 4ISQ · PDBe 4ISQ · UniProt Q9LBR1 · UniProt P21579

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