Research workbench
Structure of the pyridoxal kinase from staphylococcus aureus in complex with ADP
Analyse Structure of the pyridoxal kinase from staphylococcus aureus in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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