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Crystal structure of botulinum neurotoxin serotype D ligand binding domain in complex with N-acetylneuraminic acid

Analyse Crystal structure of botulinum neurotoxin serotype D ligand binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OBT
Type: protein
Length: 412 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Botulinum neurotoxin type D
EC: 3.4.24.69
UniProt: P19321
Ligands: SLB
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Botulinum neurotoxin type D (EC 3.4.24.69)	protein	412	8% helix, 44% strand	P19321

Ligands and binding sites

SLB · N-acetyl-beta-neuraminic acid · sugar · chains A
GOL · Glycerol · additive · 11 copies · chains A

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

Pockets

3 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	202	0.76	0.91	36	empty
2	192	0.56	0.80	31	empty
3	67	0.30	0.74	16	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3OBT · Crystal structure of Botulinum neurotoxin serotype D ligand binding domain in complex… · 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 P19321
Elsewhere: RCSB PDB 3OBT · PDBe 3OBT · UniProt P19321

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