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- PDB-8wr2: Crystal Structure of Human Pyridoxal Kinase with bound Luteolin -

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Basic information

Entry
Database: PDB / ID: 8wr2
TitleCrystal Structure of Human Pyridoxal Kinase with bound Luteolin
ComponentsPyridoxal kinase
KeywordsPROTEIN BINDING / inhibitor / Luteolin / PDXK / Complex
Function / homology
Function and homology information


pyridoxal metabolic process / pyridoxamine metabolic process / Vitamin B6 activation to pyridoxal phosphate / lithium ion binding / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / sodium ion binding / potassium ion binding / specific granule lumen ...pyridoxal metabolic process / pyridoxamine metabolic process / Vitamin B6 activation to pyridoxal phosphate / lithium ion binding / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / sodium ion binding / potassium ion binding / specific granule lumen / pyridoxal phosphate binding / secretory granule lumen / phosphorylation / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Pyridoxine kinase / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase-like
Similarity search - Domain/homology
trehalose / Chem-LU2 / Pyridoxal kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsFan, J. / Zhu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Bioorg.Chem. / Year: 2024
Title: Discovery and characterization of natural product luteolin as an effective inhibitor of human pyridoxal kinase.
Authors: Zhu, Y. / Bao, G. / Zhu, G. / Zhang, K. / Zhu, S. / Hu, J. / He, J. / Jiang, W. / Fan, J. / Dang, Y.
History
DepositionOct 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Pyridoxal kinase
A: Pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,61118
Polymers70,2872
Non-polymers2,32516
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.540, 116.110, 169.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-717-

HOH

21B-733-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules BA

#1: Protein Pyridoxal kinase


Mass: 35143.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDXK / Production host: Escherichia coli (E. coli) / References: UniProt: O00764
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 255 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-LU2 / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one / Luteolin


Mass: 286.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES pH 7.0, 66% v/v MPD, and 3% w/v D-(+)-Thehalose dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.94→47.86 Å / Num. obs: 68964 / % possible obs: 99.95 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 24.45
Reflection shellResolution: 1.94→2.009 Å / Rmerge(I) obs: 0.01265 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 68956 / CC1/2: 1 / Rpim(I) all: 0.01265 / Rrim(I) all: 0.01789

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
xia2data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YXT

2yxt


Resolution: 1.94→47.48 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 3436 4.98 %
Rwork0.1837 --
obs0.185 68958 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 154 241 5255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085098
X-RAY DIFFRACTIONf_angle_d0.9626922
X-RAY DIFFRACTIONf_dihedral_angle_d12.91695
X-RAY DIFFRACTIONf_chiral_restr0.06792
X-RAY DIFFRACTIONf_plane_restr0.009880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.970.34681110.30152617X-RAY DIFFRACTION100
1.97-1.990.27411280.262580X-RAY DIFFRACTION100
1.99-2.020.27611330.24332589X-RAY DIFFRACTION100
2.02-2.060.28381150.24412650X-RAY DIFFRACTION100
2.06-2.090.24851240.23382583X-RAY DIFFRACTION100
2.09-2.130.25751470.23272583X-RAY DIFFRACTION100
2.13-2.160.25961370.22662592X-RAY DIFFRACTION100
2.16-2.210.23971570.22062590X-RAY DIFFRACTION100
2.21-2.250.25861420.20752583X-RAY DIFFRACTION100
2.25-2.30.24171640.20932588X-RAY DIFFRACTION100
2.3-2.350.2411410.20712602X-RAY DIFFRACTION100
2.35-2.410.25031510.21432582X-RAY DIFFRACTION100
2.41-2.480.26811570.20422560X-RAY DIFFRACTION100
2.48-2.550.24641290.2112639X-RAY DIFFRACTION100
2.55-2.630.23961470.20822612X-RAY DIFFRACTION100
2.63-2.730.27951370.20582610X-RAY DIFFRACTION100
2.73-2.840.22321310.21342608X-RAY DIFFRACTION100
2.84-2.970.24051390.21512645X-RAY DIFFRACTION100
2.97-3.120.22441210.20012648X-RAY DIFFRACTION100
3.12-3.320.22561340.18532635X-RAY DIFFRACTION100
3.32-3.570.23181280.17772632X-RAY DIFFRACTION100
3.57-3.930.17611600.15962633X-RAY DIFFRACTION100
3.93-4.50.16381230.14632686X-RAY DIFFRACTION100
4.5-5.670.16561340.15612686X-RAY DIFFRACTION100

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