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HA1 (HA33) subcomponent of botulinum type C progenitor toxin complexed with N-acetylgalactosamine, bound at site II

Analyse HA1 (HA33) subcomponent of botulinum type C progenitor toxin complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AJ5
Type: protein
Length: 566 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Main hemagglutinin component
UniProt: P46084
Ligands: NGA
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Main hemagglutinin component	protein	283	10% helix, 46% strand	P46084

Ligands and binding sites

NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	230	0.54	0.77	40	empty
2	77	0.39	0.78	21	empty

Interfaces

1 interface between chains.

A–B · 1232 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3AJ5 · HA1 (HA33) subcomponent of botulinum type C progenitor toxin complexed with… · 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 P46084
Elsewhere: RCSB PDB 3AJ5 · PDBe 3AJ5 · UniProt P46084

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