MolNFT v1 · #74899 · protein
Structure of the C. difficile tcdb cysteine protease domain in complex with a peptide inhibitor
3PA8 · Toxin B: “Structure of the C. difficile tcdb cysteine protease domain in complex with a peptide inhibitor”. X-ray diffraction, 4 ligands (621, IHP, NA), 3 pockets (best druggability 0.80). MolNFT v1 #74899 on GenesisL1: 3D…
- PDB
- 3PA8
- Type
- protein
- Length
- 487 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B
- UniProt
- Q189K3
- Ligands
- 621, IHP, NA, CA
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin B | protein | 245 | 27% helix, 27% strand | Q189K3 |
| B | Toxin B | protein | 242 | 28% helix, 28% strand | Q189K3 |
Ligands and binding sites
- 621 · N-acetylglycyl-N-[(3S)-1-hydroxy-5-methyl-2-oxohexan-3-yl]-L-serinamide · ligand · 2 copies · chains A, B
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.80 | 0.82 | 96 | CA, NA, IHP |
| 2 | 89 | 0.49 | 0.82 | 20 | 621 |
| 3 | 90 | 0.49 | 0.82 | 21 | 621 |
Interfaces
1 interface between chains.
- A–B · 388 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3PA8 · Structure of the C. difficile TcdB cysteine protease domain in complex with a peptide… · 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 Q189K3
- Elsewhere: RCSB PDB 3PA8 · PDBe 3PA8 · UniProt Q189K3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.