Research workbench
Crystal structure of mouse pyridoxal kinase in apo form
Analyse Crystal structure of mouse pyridoxal kinase in apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YJZ
- Type
- protein
- Length
- 1,216 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase | protein | 304 | 40% helix, 20% strand | — |
| B | Pyridoxal kinase | protein | 308 | 41% helix, 22% strand | — |
| C | Pyridoxal kinase | protein | 302 | 42% helix, 20% strand | — |
| D | Pyridoxal kinase | protein | 302 | 41% helix, 21% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.77 | 0.79 | 89 | EDO |
| 2 | 692 | 0.76 | 0.81 | 61 | PG4, EDO |
| 3 | 609 | 0.74 | 0.81 | 53 | EDO |
| 4 | 50 | 0.71 | 0.99 | 16 | empty |
| 5 | 631 | 0.71 | 0.78 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1926 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1881 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 376 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 78 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6YJZ · Crystal structure of mouse pyridoxal kinase in apo form · 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
- Elsewhere: RCSB PDB 6YJZ · PDBe 6YJZ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.