MolNFT v1 · #87582 · protein
Structure of the pyridoxal kinase from staphylococcus aureus in complex with ADP
4C5K · Phosphomethylpyrimidine kinase: “Structure of the pyridoxal kinase from staphylococcus aureus in complex with ADP”. X-ray diffraction, 2 ligands (ADP, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #87582 on GenesisL1: 3D…
- PDB
- 4C5K
- Type
- protein
- Length
- 1,094 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
- ADP, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 274 | 41% helix, 23% strand | Q99W31 |
| C | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 270 | 41% helix, 23% strand | Q99W31 |
| D | Phosphomethylpyrimidine kinase (EC 2.7.1.35) | protein | 276 | 41% helix, 24% strand | Q99W31 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.78 | 0.81 | 93 | empty |
| 2 | 743 | 0.77 | 0.81 | 93 | ADP, SO4 |
| 3 | 617 | 0.70 | 0.78 | 64 | ADP, SO4 |
| 4 | 567 | 0.70 | 0.78 | 56 | ADP, SO4 |
| 5 | 282 | 0.67 | 0.82 | 45 | ADP, SO4 |
Interfaces
5 interfaces between chains.
- B–D · 1969 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1951 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 273 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 255 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4C5K · Structure of the pyridoxal kinase from Staphylococcus aureus in complex with ADP · 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 4C5K · PDBe 4C5K · UniProt Q99W31
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