Research workbench
Crystal structure of pyridoxamine kinase pdxy from burkholderia xenovorans
Analyse Crystal structure of pyridoxamine kinase pdxy from burkholderia xenovorans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TRW
- Type
- protein
- Length
- 278 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase pdxy
- EC
- 2.7.1.35
- UniProt
- Q141E8
- Ligands
- NO3, CL, SO4
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase pdxy (EC 2.7.1.35) | protein | 278 | 42% helix, 20% strand | Q141E8 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.60 | 0.76 | 42 | NO3 |
| 2 | 65 | 0.35 | 0.76 | 9 | NHE |
Compared structures
- 5TRW · Crystal structure of Pyridoxamine kinase PDXY from Burkholderia xenovorans · the same entry in another collection · chain A against A, TM-score 1.00
- Q141E8 · AlphaFold monomer V2.0 prediction for pyridoxal kinase pdxy (Q141E8) · a predicted model of the same protein · 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 Q141E8
- Elsewhere: RCSB PDB 5TRW · PDBe 5TRW · UniProt Q141E8
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