Research workbench
Crystal structure of C-terminal domain of shaft pilin spaa from lactobacillus rhamnosus gg - P21212 space group with yb heavy atom
Analyse Crystal structure of C-terminal domain of shaft pilin spaa from lactobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FGR
- Type
- protein
- Length
- 486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell surface protein spaa
- UniProt
- C7T9P4
- Ligands
- YB
- Pockets
- 10 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell surface protein spaa | protein | 121 | 2% helix, 46% strand | C7T9P4 |
| B | Cell surface protein spaa | protein | 121 | 6% helix, 44% strand | C7T9P4 |
| C, D | Cell surface protein spaa | protein | 122 | 6% helix, 48% strand | C7T9P4 |
Ligands and binding sites
- YB · Ytterbium (III) ion · metal · 10 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.55 | 0.76 | 44 | empty |
| 2 | 272 | 0.55 | 0.76 | 45 | empty |
| 3 | 176 | 0.48 | 0.77 | 33 | empty |
| 4 | 142 | 0.44 | 0.76 | 30 | empty |
| 5 | 94 | 0.42 | 0.78 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–C · 574 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 550 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 508 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 452 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 5FGR · Crystal structure of C-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus… · 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 C7T9P4
- Elsewhere: RCSB PDB 5FGR · PDBe 5FGR · UniProt C7T9P4
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