Research workbench
Crystal structure of pyridoxal kinase (pdxk) from salmonella typhimurium in complex with ADP, pl-linked to LYS233 via a schiff base
Analyse Crystal structure of pyridoxal kinase (pdxk) from salmonella typhimurium in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZWB
- Type
- protein
- Length
- 541 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PYRIDOXINE/PYRIDOXAL/PYRIDOXAMINE kinase
- EC
- 2.7.1.35
- UniProt
- A0A0M0PWM4
- Ligands
- ADP, MG, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PYRIDOXINE/PYRIDOXAL/PYRIDOXAMINE kinase (EC 2.7.1.35) | protein | 271 | 39% helix, 21% strand | A0A0M0PWM4 |
| B | PYRIDOXINE/PYRIDOXAL/PYRIDOXAMINE kinase (EC 2.7.1.35) | protein | 270 | 40% helix, 20% strand | A0A0M0PWM4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.80 | 0.82 | 75 | EDO |
| 2 | 715 | 0.75 | 0.80 | 50 | TRS, EDO |
| 3 | 383 | 0.69 | 0.81 | 42 | MG, ADP, EDO |
Interfaces
1 interface between chains.
- A–B · 1762 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact, nonstandard).
Compared structures
- 5ZWB · Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with… · 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 A0A0M0PWM4
- Elsewhere: RCSB PDB 5ZWB · PDBe 5ZWB · UniProt A0A0M0PWM4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.