MolNFT v1 · #169275 · protein
Crystal structure of inactive enzymatic binary toxin component from clostridium difficile in complex with NADPH
6X6V · Cdta: “Crystal structure of inactive enzymatic binary toxin component from clostridium difficile in complex with…”. X-ray diffraction, 1 ligand (NDP), 16 pockets (best druggability 0.74). MolNFT v1 #169275 on GenesisL1: 3D…
- 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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