MolNFT v1 · #135153 · protein
Crystal structure of a pyridoxal kinase from burkholderia multivorans
5TQI · Pyridoxal kinase pdxy: “Crystal structure of a pyridoxal kinase from burkholderia multivorans”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.76). MolNFT v1 #135153 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5TQI
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase pdxy
- EC
- 2.7.1.35
- UniProt
- A0A0H3KDL9
- Ligands
- CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase pdxy (EC 2.7.1.35) | protein | 288 | 41% helix, 20% strand | A0A0H3KDL9 |
| B | Pyridoxal kinase pdxy (EC 2.7.1.35) | protein | 287 | 39% helix, 20% strand | A0A0H3KDL9 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.76 | 0.90 | 45 | empty |
| 2 | 331 | 0.66 | 0.81 | 41 | empty |
| 3 | 390 | 0.64 | 0.78 | 45 | CL |
| 4 | 57 | 0.57 | 0.90 | 16 | CL |
| 5 | 122 | 0.46 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1695 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5TQI · Crystal structure of a pyridoxal kinase from Burkholderia multivorans · 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 A0A0H3KDL9
- Elsewhere: RCSB PDB 5TQI · PDBe 5TQI · UniProt A0A0H3KDL9
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