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Crystal structure of a catalytically active, non-toxic endopeptidase derivative of clostridium botulinum toxin a
Analyse Crystal structure of a catalytically active, non-toxic endopeptidase derivative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W2D
- Type
- protein
- Length
- 1,701 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin a light chain; Botulinum neurotoxin a heavy chain
- EC
- 3.4.24.69
- UniProt
- A5HZZ9
- Ligands
- ZN, SO4, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin a light chain (EC 3.4.24.69) | protein | 436 | 30% helix, 18% strand | A5HZZ9 |
| B | Botulinum neurotoxin a heavy chain (EC 3.4.24.69) | protein | 423 | 53% helix, 7% strand | A5HZZ9 |
| C | Botulinum neurotoxin a light chain (EC 3.4.24.69) | protein | 435 | 29% helix, 18% strand | A5HZZ9 |
| D | Botulinum neurotoxin a heavy chain (EC 3.4.24.69) | protein | 407 | 50% helix, 7% strand | A5HZZ9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, D
- GOL · Glycerol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.87 | 0.90 | 82 | empty |
| 2 | 726 | 0.87 | 0.91 | 88 | empty |
| 3 | 908 | 0.85 | 0.87 | 84 | empty |
| 4 | 1101 | 0.81 | 0.82 | 75 | ZN |
| 5 | 1138 | 0.80 | 0.81 | 73 | empty |
Interfaces
6 interfaces between chains.
- C–D · 5417 Ų buried · 85 hydrogen bonds · protein-protein
- A–B · 5383 Ų buried · 93 hydrogen bonds · protein-protein
- B–D · 605 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 561 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2W2D · Crystal Structure of a Catalytically Active, Non-toxic Endopeptidase Derivative of… · 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 A5HZZ9
- Elsewhere: RCSB PDB 2W2D · PDBe 2W2D · UniProt A5HZZ9
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