MolNFT v1 · #118926 · protein
Crystal structure of C-terminal domain of shaft pilin spaa from lactobacillus rhamnosus gg - P21212 space group
5FGS · Cell surface protein spaa: “Crystal structure of C-terminal domain of shaft pilin spaa from lactobacillus rhamnosus gg - P21212 space…”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.50). MolNFT v1 #118926 on…
- PDB
- 5FGS
- Type
- protein
- Length
- 493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell surface protein spaa
- UniProt
- C7T9P4
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Cell surface protein spaa | protein | 123 | 6% helix, 47% strand | C7T9P4 |
| C | Cell surface protein spaa | protein | 124 | 6% helix, 47% strand | C7T9P4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.50 | 0.78 | 29 | empty |
| 2 | 168 | 0.48 | 0.77 | 27 | empty |
| 3 | 160 | 0.47 | 0.77 | 28 | empty |
| 4 | 128 | 0.43 | 0.76 | 23 | empty |
| 5 | 73 | 0.42 | 0.80 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 604 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 558 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 548 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 5FGS · 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 5FGS · PDBe 5FGS · UniProt C7T9P4
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