MolNFT v1 · #40792 · protein
Crystal structure of the enzymatic component C2-I of the C2-toxin from clostridium botulinum at pH 6.1
2J3Z · C2 toxin component I: “Crystal structure of the enzymatic component C2-I of the C2-toxin from clostridium botulinum at pH 6.1”. X-ray diffraction, 2 ligands (CO, SO4), 20 pockets (best druggability 0.85). MolNFT v1 #40792 on…
- PDB
- 2J3Z
- Type
- protein
- Length
- 2,553 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C2 toxin component I
- UniProt
- O69275
- Ligands
- CO, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C2 toxin component I | protein | 430 | 34% helix, 27% strand | O69275 |
| C | C2 toxin component I | protein | 428 | 36% helix, 28% strand | O69275 |
| D, F | C2 toxin component I | protein | 421 | 36% helix, 26% strand | O69275 |
| E | C2 toxin component I | protein | 423 | 35% helix, 28% strand | O69275 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 7 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 40 copies · chains A, F, B, D, C, E
- GOL · Glycerol · additive · 12 copies · chains A, F, B, D, C, E
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 | 1096 | 0.85 | 0.86 | 99 | GOL, SO4 |
| 2 | 1139 | 0.85 | 0.86 | 114 | GOL, SO4 |
| 3 | 1060 | 0.84 | 0.85 | 102 | GOL, SO4 |
| 4 | 653 | 0.72 | 0.79 | 64 | empty |
| 5 | 663 | 0.72 | 0.79 | 62 | CO |
Interfaces
9 interfaces between chains.
- B–D · 1400 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 1389 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 1325 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 903 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 894 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2J3Z · Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium… · 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 O69275
- Elsewhere: RCSB PDB 2J3Z · PDBe 2J3Z · UniProt O69275
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