MolNFT v1 · #109920 · protein
Crystal structure of salmonella typhimurium propionate kinase in complex with amppnp and propionate
4XH1: “Crystal structure of salmonella typhimurium propionate kinase in complex with amppnp and propionate”. X-ray diffraction, 1 ligand (ANP), 3 pockets (best druggability 0.55). MolNFT v1 #109920 on GenesisL1: 3D structure, binding sites…
- PDB
- 4XH1
- Type
- protein
- Length
- 393 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propionate kinase
- EC
- 2.7.2.15
- UniProt
- O06961
- Ligands
- ANP
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Propionate kinase (EC 2.7.2.15) | protein | 393 | 44% helix, 19% strand | O06961 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PPI · Propanoic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.55 | 0.75 | 38 | PPI |
| 2 | 195 | 0.47 | 0.74 | 19 | empty |
| 3 | 55 | 0.34 | 0.78 | 16 | empty |
Compared structures
- 4XH1 · Crystal structure of Salmonella typhimurium propionate kinase in complex with AMPPNP and… · the same entry in another collection · chain A against A, TM-score 1.00
- O06961 · AlphaFold monomer V2.0 prediction for propionate kinase (O06961) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O06961
- Elsewhere: RCSB PDB 4XH1 · PDBe 4XH1 · UniProt O06961
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