Research workbench
X-ray structure of major pilin from C. perfringens SM101
Analyse X-ray structure of major pilin from C. perfringens SM101 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IXY
- Type
- protein
- Length
- 1,804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.72
- Source
- Clostridium perfringens (strain SM101 / Type A)
- Molecule
- pilin
- UniProt
- Q0SWL8
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.72 · 2 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | pilin | protein | 448 | 8% helix, 48% strand | Q0SWL8 |
| B, D | pilin | protein | 454 | 7% helix, 47% strand | Q0SWL8 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.61 | 0.80 | 31 | empty |
| 2 | 317 | 0.61 | 0.78 | 36 | empty |
| 3 | 290 | 0.58 | 0.78 | 34 | empty |
| 4 | 275 | 0.58 | 0.78 | 39 | empty |
| 5 | 216 | 0.53 | 0.77 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–D · 813 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 799 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 724 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 712 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 isopeptide (isopeptide).
Compared structures
- 6IXY · X-ray structure of major pilin from C. perfringens SM101 · 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 Q0SWL8
- Elsewhere: RCSB PDB 6IXY · PDBe 6IXY · UniProt Q0SWL8
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