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Crystal structure of human pl kinase with bound plp and ATP
Analyse Crystal structure of human pl kinase with bound plp and ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KEU
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase
- EC
- 2.7.1.35
- UniProt
- O00764
- Ligands
- ATP, PLP, MG, NA, SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase (EC 2.7.1.35) | protein | 305 | 40% helix, 20% strand | O00764 |
| B | Pyridoxal kinase (EC 2.7.1.35) | protein | 305 | 42% helix, 23% strand | O00764 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.78 | 0.81 | 65 | MG, NA, ATP, PLP, MPD |
| 2 | 725 | 0.77 | 0.82 | 56 | MG, NA, ATP, MPD, PLP |
| 3 | 79 | 0.76 | 0.99 | 16 | empty |
| 4 | 106 | 0.62 | 0.88 | 16 | empty |
| 5 | 72 | 0.47 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2237 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
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 O00764
- Elsewhere: RCSB PDB 3KEU · PDBe 3KEU · UniProt O00764
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