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- PDB-7qdn: Structure of human liver pyruvate kinase from which the B domain ... -

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Basic information

Entry
Database: PDB / ID: 7qdn
TitleStructure of human liver pyruvate kinase from which the B domain has been deleted
ComponentsPyruvate kinase PKLR
KeywordsTRANSFERASE / PKL / PYRUVATE KINASE / GLYCOLYSIS
Function / homology
Function and homology information


pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / response to metal ion / monosaccharide binding / Glycolysis / response to ATP ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / response to metal ion / monosaccharide binding / Glycolysis / response to ATP / potassium ion binding / Regulation of gene expression in beta cells / response to glucose / response to cAMP / cellular response to epinephrine stimulus / response to nutrient / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / phosphorylation / magnesium ion binding / extracellular exosome / ATP binding / cytoplasm / cytosol
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / : / OXALIC ACID / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsLulla, A. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase.
Authors: Nain-Perez, A. / Foller Fuchtbauer, A. / Haversen, L. / Lulla, A. / Gao, C. / Matic, J. / Monjas, L. / Rodriguez, A. / Brear, P. / Kim, W. / Hyvonen, M. / Boren, J. / Mardinoglu, A. / Uhlen, M. / Grotli, M.
History
DepositionNov 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvate kinase PKLR
B: Pyruvate kinase PKLR
C: Pyruvate kinase PKLR
D: Pyruvate kinase PKLR
E: Pyruvate kinase PKLR
F: Pyruvate kinase PKLR
G: Pyruvate kinase PKLR
H: Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,36946
Polymers386,2838
Non-polymers4,08638
Water46,1542562
1
A: Pyruvate kinase PKLR
B: Pyruvate kinase PKLR
C: Pyruvate kinase PKLR
D: Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,18523
Polymers193,1424
Non-polymers2,04319
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22320 Å2
ΔGint-181 kcal/mol
Surface area56890 Å2
2
E: Pyruvate kinase PKLR
F: Pyruvate kinase PKLR
G: Pyruvate kinase PKLR
H: Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,18523
Polymers193,1424
Non-polymers2,04319
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22100 Å2
ΔGint-183 kcal/mol
Surface area56200 Å2
Unit cell
Length a, b, c (Å)207.448, 112.687, 188.333
Angle α, β, γ (deg.)90.000, 91.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
Pyruvate kinase PKLR / Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver ...Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver pyruvate kinase


Mass: 48285.379 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKLR, PK1, PKL / Plasmid: pExp-NHis / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30613, pyruvate kinase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 2592 molecules

#3: Chemical
ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H2O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2562 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES/MOPS, 10% PEG8000, 20% ethylene glycol, 10 mM phenylalanine, 20 mM sodium oxalate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 1.695→103.695 Å / Num. obs: 447443 / % possible obs: 93.5 % / Redundancy: 15.3 % / Biso Wilson estimate: 36.07 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 14.5
Reflection shellResolution: 1.695→1.725 Å / Redundancy: 13.4 % / Rmerge(I) obs: 4.784 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 22972 / Rsym value: 4.784 / % possible all: 96.3

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ip7

4ip7


Resolution: 1.695→103.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.096
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 22295 5.03 %RANDOM
Rwork0.2053 ---
obs0.2059 443259 92.6 %-
Displacement parametersBiso max: 120.75 Å2 / Biso mean: 41.37 Å2 / Biso min: 21.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.6941 Å20 Å2-7.2386 Å2
2--2.6558 Å20 Å2
3----0.9617 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.695→103.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25896 0 230 2562 28688
Biso mean--35.84 44.18 -
Num. residues----3415
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9476SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4602HARMONIC5
X-RAY DIFFRACTIONt_it26683HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3592SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact24240SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d26683HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg36166HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion16.04
LS refinement shellResolution: 1.7→1.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3853 436 4.92 %
Rwork0.3893 8430 -
all0.3891 8866 -
obs--74.18 %

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