Research workbench
The structure of pilj, a type IV pilin from clostridium difficile
Analyse The structure of pilj, a type IV pilin from clostridium difficile in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IXJ
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fimbrial protein (pilin)
- UniProt
- C9YJD3
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fimbrial protein (pilin) | protein | 224 | 38% helix, 20% strand | C9YJD3 |
| B | Fimbrial protein (pilin) | protein | 228 | 38% helix, 21% strand | C9YJD3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.65 | 0.80 | 51 | GOL |
| 2 | 183 | 0.63 | 0.84 | 29 | GOL |
| 3 | 312 | 0.56 | 0.76 | 39 | GOL |
| 4 | 106 | 0.35 | 0.73 | 18 | empty |
| 5 | 65 | 0.31 | 0.75 | 14 | GOL |
Interfaces
1 interface between chains.
- A–B · 465 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4IXJ · The structure of PilJ, a Type IV pilin from Clostridium difficile · 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 C9YJD3
- Elsewhere: RCSB PDB 4IXJ · PDBe 4IXJ · UniProt C9YJD3
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