MolNFT v1 · #140459 · protein
Structural of the highly conserved ATPase from type III secretion system of bacterial pathogens
5YBH · Probable ATP synthase SPAL/MXIB: “Structural of the highly conserved ATPase from type III secretion system of bacterial pathogens”. X-ray diffraction, 2 ligands (MG, SO4), 12 pockets (best druggability 0.61). MolNFT v1 #140459 on…
- PDB
- 5YBH
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP synthase SPAL/MXIB
- EC
- 3.6.3.14
- UniProt
- P0A1C1
- Ligands
- MG, SO4
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP synthase SPAL/MXIB (EC 3.6.3.14) | protein | 334 | 43% helix, 21% strand | P0A1C1 |
| B | Probable ATP synthase SPAL/MXIB (EC 3.6.3.14) | protein | 340 | 44% helix, 20% strand | P0A1C1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 20 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.61 | 0.83 | 20 | empty |
| 2 | 193 | 0.60 | 0.82 | 27 | empty |
| 3 | 211 | 0.56 | 0.79 | 27 | MG |
| 4 | 140 | 0.48 | 0.78 | 22 | MG |
| 5 | 64 | 0.48 | 0.84 | 14 | MG |
Interfaces
1 interface between chains.
- A–B · 585 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5YBH · Structural of the highly conserved ATPase from type III secretion system of bacterial… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A1C1 · AlphaFold monomer V2.0 prediction for type 3 secretion system ATPase (P0A1C1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A1C1
- Elsewhere: RCSB PDB 5YBH · PDBe 5YBH · UniProt P0A1C1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.