MolNFT v1 · #11804 · protein
4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from salmonella typhimurium complexed with 4-amino-5- hydroxymethyl-2-methylpyrimidine
1JXI · Phosphomethylpyrimidine kinase: “4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from salmonella typhimurium complexed with…”. X-ray diffraction, 2 ligands (HMH, SO4), 4 pockets (best druggability 0.68). MolNFT v1 #11804…
- PDB
- 1JXI
- Type
- protein
- Length
- 508 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
- HMH, SO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphomethylpyrimidine kinase (EC 2.7.4.7) | protein | 254 | 41% helix, 20% strand | P55882 |
Ligands and binding sites
- HMH · 4-amino-5-hydroxymethyl-2-methylpyrimidine · ligand · 2 copies · chains A, B
- 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.68 | 0.96 | 18 | empty |
| 2 | 50 | 0.65 | 0.95 | 18 | empty |
| 3 | 343 | 0.64 | 0.79 | 48 | SO4, HMH |
| 4 | 366 | 0.64 | 0.79 | 46 | SO4, HMH |
Interfaces
1 interface between chains.
- A–B · 2334 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 1JXI · 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 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 P55882
- Elsewhere: RCSB PDB 1JXI · PDBe 1JXI · UniProt P55882
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