MolNFT v1 · #87581 · protein
Structure of the pyridoxal kinase from staphylococcus aureus
4C5J · Phosphomethylpyrimidine kinase: “Structure of the pyridoxal kinase from staphylococcus aureus”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.85). MolNFT v1 #87581 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4C5J
- Type
- protein
- Length
- 1,099 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomethylpyrimidine kinase
- EC
- 2.7.1.35
- UniProt
- Q99W31
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 276 | 41% helix, 24% strand | Q99W31 |
| D | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 271 | 41% helix, 23% strand | Q99W31 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.85 | 0.85 | 131 | SO4 |
| 2 | 613 | 0.70 | 0.78 | 65 | SO4 |
| 3 | 178 | 0.69 | 0.88 | 23 | SO4 |
| 4 | 496 | 0.68 | 0.79 | 56 | SO4 |
| 5 | 146 | 0.60 | 0.84 | 23 | SO4 |
Interfaces
5 interfaces between chains.
- A–D · 1946 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1944 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 360 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 122 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4C5J · Structure of the pyridoxal kinase from Staphylococcus aureus · the same entry in another collection · 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 Q99W31
- Elsewhere: RCSB PDB 4C5J · PDBe 4C5J · UniProt Q99W31
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