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Structural of the highly conserved ATPase from type III secretion system of bacterial pathogens
Analyse Structural of the highly conserved ATPase from type III secretion system of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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