Research workbench
Crystal structure of enzymatic binary toxin component from clostridium difficile in complex with
Analyse Crystal structure of enzymatic binary toxin component from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X6X
- Type
- protein
- Length
- 833 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyltransferase
- UniProt
- F5B5W8
- Ligands
- UTG, ZN
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyltransferase | protein | 417 | 37% helix, 27% strand | F5B5W8 |
| B | ADP-ribosyltransferase | protein | 416 | 37% helix, 27% strand | F5B5W8 |
Ligands and binding sites
- UTG · N-(2-chlorophenyl)-N'-[(furan-2-yl)methyl]thiourea · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.65 | 0.76 | 40 | empty |
| 2 | 588 | 0.65 | 0.76 | 38 | empty |
| 3 | 457 | 0.62 | 0.76 | 62 | empty |
| 4 | 51 | 0.60 | 0.93 | 24 | empty |
| 5 | 93 | 0.59 | 0.87 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1115 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6X6X · Crystal structure of enzymatic binary toxin component from Clostridium difficile in… · 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 F5B5W8
- Elsewhere: RCSB PDB 6X6X · PDBe 6X6X · UniProt F5B5W8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.