Research workbench
Crystal structure of inactive enzymatic binary toxin component from clostridium difficile in complex with NADPH
Analyse Crystal structure of inactive 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
- 6X6V
- Type
- protein
- Length
- 1,664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdta
- UniProt
- F5B5W8
- Ligands
- NDP
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cdta | protein | 416 | 39% helix, 28% strand | F5B5W8 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.74 | 0.77 | 124 | NDP |
| 2 | 56 | 0.70 | 0.97 | 23 | empty |
| 3 | 465 | 0.67 | 0.79 | 57 | empty |
| 4 | 507 | 0.64 | 0.76 | 41 | empty |
| 5 | 496 | 0.63 | 0.76 | 39 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1071 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1042 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 383 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 216 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6X6V · Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile… · the same entry in another collection · chain D against D, 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 6X6V · PDBe 6X6V · UniProt F5B5W8
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