Research workbench
Crystal structure of pilus adhesin, SpaC from Lactobacillus rhamnosus GG - P21212 form
Analyse Crystal structure of pilus adhesin, SpaC from Lactobacillus rhamnosus GG… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M48
- Type
- protein
- Length
- 1,625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Lactobacillus rhamnosus GG
- Molecule
- SpaC
- UniProt
- A0A1Y0DVK9
- Ligands
- MG, CL
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SpaC | protein | 813 | 12% helix, 46% strand | A0A1Y0DVK9 |
| B | SpaC | protein | 812 | 13% helix, 45% strand | A0A1Y0DVK9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.63 | 0.77 | 36 | empty |
| 2 | 84 | 0.55 | 0.86 | 27 | empty |
| 3 | 200 | 0.51 | 0.77 | 22 | empty |
| 4 | 154 | 0.46 | 0.76 | 25 | MG |
| 5 | 119 | 0.45 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 381 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 isopeptide (isopeptide).
Compared structures
- 6M48 · Crystal structure of pilus adhesin, spac from lactobacillus rhamnosus gg - P21212 form · 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 A0A1Y0DVK9
- Elsewhere: RCSB PDB 6M48 · PDBe 6M48 · UniProt A0A1Y0DVK9
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