Research workbench
4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from salmonella typhimurium
Analyse 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JXH
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomethylpyrimidine kinase
- EC
- 2.7.4.7
- UniProt
- P55882
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphomethylpyrimidine kinase (EC 2.7.4.7) | protein | 248 | 42% helix, 21% strand | P55882 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.56 | 0.75 | 49 | SO4 |
| 2 | 255 | 0.52 | 0.76 | 34 | SO4 |
| 3 | 101 | 0.37 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2299 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 1JXH · 4-Amino-5-hydroxymethyl-2-methylpyrimidine Phosphate Kinase from Salmonella typhimurium · the same entry in another collection · chain A against A, TM-score 1.00
- P55882 · AlphaFold monomer V2.0 prediction for HYDROXYMETHYLPYRIMIDINE/PHOSPHOMETHYLPYRIMIDINE… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P55882
- Elsewhere: RCSB PDB 1JXH · PDBe 1JXH · UniProt P55882
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