Research workbench
Crystal structure of HA70 (HA3) subcomponent of clostridium botulinum type C progenitor toxin in complex with alpha 2-6-sialyllactosamine
Analyse Crystal structure of HA70 (HA3) subcomponent of clostridium botulinum type C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EN9
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin components ha-22/23/53
- UniProt
- P46085
- Ligands
- NAG, GAL, SIA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin components ha-22/23/53 | protein | 170 | 9% helix, 48% strand | P46085 |
| B | Hemagglutinin components ha-22/23/53 | protein | 420 | 5% helix, 47% strand | P46085 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- GAL · beta-D-galactopyranose · sugar · chains B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.72 | 0.93 | 36 | empty |
| 2 | 118 | 0.55 | 0.84 | 25 | empty |
| 3 | 209 | 0.54 | 0.78 | 35 | MRD |
| 4 | 55 | 0.44 | 0.83 | 16 | empty |
| 5 | 84 | 0.37 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2189 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 4EN9 · Crystal structure of HA70 (HA3) subcomponent of Clostridium botulinum type C progenitor… · 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 P46085
- Elsewhere: RCSB PDB 4EN9 · PDBe 4EN9 · UniProt P46085
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