MolNFT v1 · #140460 · protein
Structure of the bacterial pathogens ATPase with substrate amppnp
5YBI · Probable ATP synthase SPAL/MXIB: “Structure of the bacterial pathogens ATPase with substrate amppnp”. X-ray diffraction, 3 ligands (ANP, MG, SO4), 9 pockets (best druggability 0.61). MolNFT v1 #140460 on GenesisL1: 3D structure…
- PDB
- 5YBI
- Type
- protein
- Length
- 682 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
- ANP, MG, SO4
- Pockets
- 9 · 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 | 337 | 45% helix, 20% strand | P0A1C1 |
| B | Probable ATP synthase SPAL/MXIB (EC 3.6.3.14) | protein | 345 | 44% helix, 20% strand | P0A1C1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 38 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.61 | 0.79 | 32 | empty |
| 2 | 174 | 0.58 | 0.81 | 24 | MG |
| 3 | 157 | 0.55 | 0.80 | 26 | MG |
| 4 | 137 | 0.48 | 0.78 | 21 | MG |
| 5 | 148 | 0.44 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5YBI · Structure of the bacterial pathogens ATPase with substrate AMPPNP · 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 5YBI · PDBe 5YBI · UniProt P0A1C1
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