Research workbench
Crystal structure of the catalytic domain of the weissela oryzae botulinum like toxin
Analyse Crystal structure of the catalytic domain of the weissela oryzae botulinum like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RIM
- Type
- protein
- Length
- 3,586 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative botulinum-like toxin wo
- EC
- 3.4.24.69
- UniProt
- A0A069CUU9
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative botulinum-like toxin wo (EC 3.4.24.69) | protein | 441 | 30% helix, 20% strand | A0A069CUU9 |
| B | Putative botulinum-like toxin wo (EC 3.4.24.69) | protein | 442 | 29% helix, 20% strand | A0A069CUU9 |
| C | Putative botulinum-like toxin wo (EC 3.4.24.69) | protein | 440 | 30% helix, 21% strand | A0A069CUU9 |
| D | Putative botulinum-like toxin wo (EC 3.4.24.69) | protein | 439 | 30% helix, 20% strand | A0A069CUU9 |
| E | Putative botulinum-like toxin wo (EC 3.4.24.69) | protein | 457 | 29% helix, 22% strand | A0A069CUU9 |
| F, H | Putative botulinum-like toxin wo (EC 3.4.24.69) | protein | 458 | 28% helix, 22% strand | A0A069CUU9 |
| G | Putative botulinum-like toxin wo (EC 3.4.24.69) | protein | 451 | 29% helix, 22% strand | A0A069CUU9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.76 | 0.78 | 81 | empty |
| 2 | 520 | 0.72 | 0.81 | 75 | CA |
| 3 | 499 | 0.72 | 0.81 | 74 | CA |
| 4 | 465 | 0.72 | 0.82 | 68 | CA |
| 5 | 493 | 0.71 | 0.81 | 75 | CA |
Interfaces
14 interfaces between chains.
- D–F · 630 Ų buried · 9 hydrogen bonds · protein-protein
- E–H · 591 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 588 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 585 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 577 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 6RIM · Crystal structure of the catalytic domain of the Weissela oryzae botulinum like toxin · 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 A0A069CUU9
- Elsewhere: RCSB PDB 6RIM · PDBe 6RIM · UniProt A0A069CUU9
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