MolNFT v1 · #162766 · protein
Crystal structure of the catalytic domain of the weissela oryzae botulinum like toxin
6RIM · Putative botulinum-like toxin wo: “Crystal structure of the catalytic domain of the weissela oryzae botulinum like toxin”. X-ray diffraction, 2 ligands (ZN, CA), 20 pockets (best druggability 0.76). MolNFT v1 #162766 on GenesisL1…
- 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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