MolNFT v1 · #120783 · protein
Crystal structure of shaft pilin spaa from lactobacillus rhamnosus gg - E139A mutant
5HBB · Cell surface protein spaa: “Crystal structure of shaft pilin spaa from lactobacillus rhamnosus gg - E139A mutant”. X-ray diffraction, 2 ligands (NA, SCN), 8 pockets (best druggability 0.54). MolNFT v1 #120783 on GenesisL1: 3D…
- PDB
- 5HBB
- Type
- protein
- Length
- 796 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell surface protein spaa
- UniProt
- C7T9P4
- Ligands
- NA, SCN
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cell surface protein spaa | protein | 264 | 6% helix, 42% strand | C7T9P4 |
| A | Cell surface protein spaa | protein | 265 | 6% helix, 42% strand | C7T9P4 |
| C | Cell surface protein spaa | protein | 267 | 6% helix, 42% strand | C7T9P4 |
Ligands and binding sites
- NA · Sodium ion · metal · 17 copies · chains B, A, C
- SCN · Thiocyanate ion · ion · 3 copies · chains B, A, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.54 | 0.89 | 15 | EDO |
| 2 | 90 | 0.50 | 0.82 | 23 | EDO |
| 3 | 113 | 0.46 | 0.78 | 28 | EDO |
| 4 | 90 | 0.37 | 0.75 | 19 | empty |
| 5 | 69 | 0.33 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 746 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 677 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 isopeptide (isopeptide).
Compared structures
- 5HBB · Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - E139A mutant · the same entry in another collection · chain B against B, 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 5HBB · PDBe 5HBB · UniProt C7T9P4
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