Research workbench
Crystal structure of salmonella typhimurium yegs, a putative lipid kinase homologous to eukaryotic sphingosine and diacylglycerol kinases.
Analyse Crystal structure of salmonella typhimurium yegs, a putative lipid kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P1R
- Type
- protein
- Length
- 1,146 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipid kinase yegs
- EC
- 2.7.1.-
- UniProt
- Q8ZNP1
- Ligands
- CA, NA, CL
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipid kinase yegs (EC 2.7.1.-) | protein | 290 | 25% helix, 37% strand | Q8ZNP1 |
| C, D | Lipid kinase yegs (EC 2.7.1.-) | protein | 283 | 25% helix, 37% strand | Q8ZNP1 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.77 | 0.80 | 97 | CA |
| 2 | 944 | 0.77 | 0.80 | 103 | CA |
| 3 | 559 | 0.67 | 0.78 | 43 | empty |
| 4 | 350 | 0.61 | 0.78 | 44 | empty |
| 5 | 353 | 0.59 | 0.77 | 40 | empty |
Interfaces
5 interfaces between chains.
- B–C · 848 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 827 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 325 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 322 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 2P1R · Crystal structure of Salmonella typhimurium YegS, a putative lipid kinase homologous to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZNP1 · AlphaFold monomer V2.0 prediction for probable lipid kinase yegs (Q8ZNP1) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q8ZNP1
- Elsewhere: RCSB PDB 2P1R · PDBe 2P1R · UniProt Q8ZNP1
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