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- PDB-7qzu: Structure of liver pyruvate kinase in complex with anthraquinone ... -

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Basic information

Entry
Database: PDB / ID: 7qzu
TitleStructure of liver pyruvate kinase in complex with anthraquinone derivative 47
ComponentsPKL
KeywordsTRANSFERASE / Pyruvate kinase / active site / inhibition
Function / homology1,6-di-O-phosphono-beta-D-fructofuranose / Chem-I4L / : / OXALATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.964 Å
AuthorsLulla, A. / Foller, A. / Nain-Perez, A. / Grotli, M. / Brear, P. / 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
DepositionJan 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 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

Downloads & links

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Assembly

Deposited unit
A: PKL
B: PKL
C: PKL
D: PKL
E: PKL
F: PKL
G: PKL
H: PKL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,59046
Polymers386,2838
Non-polymers7,30738
Water45,4522523
1
A: PKL
B: PKL
C: PKL
D: PKL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,79523
Polymers193,1424
Non-polymers3,65419
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21890 Å2
ΔGint-132 kcal/mol
Surface area56450 Å2
2
E: PKL
F: PKL
G: PKL
H: PKL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,79523
Polymers193,1424
Non-polymers3,65419
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21790 Å2
ΔGint-133 kcal/mol
Surface area56000 Å2
Unit cell
Length a, b, c (Å)207.629, 112.593, 188.797
Angle α, β, γ (deg.)90.000, 91.580, 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
PKL


Mass: 48285.379 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEXP-NHis / Production host: Escherichia coli BL21(DE3) (bacteria)
#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, 2553 molecules

#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / 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-I4L / (2~{S})-2-[2-[4-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]sulfonylpiperazin-1-yl]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid


Mass: 562.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H22N2O12S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2523 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
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: 0.9587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9587 Å / Relative weight: 1
ReflectionResolution: 1.964→188.725 Å / Num. obs: 237404 / % possible obs: 94.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsCC1/2Rpim(I) all
2.002-2.1367.57.51.2621.688446118640.6340.496
5.866-188.72599.86.70.03632.578938118620.9990.015

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (16-JUL-2021)refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.25data extraction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QDN

7qdn


Resolution: 1.964→188.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.22 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.17
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 11829 4.98 %RANDOM
Rwork0.2014 ---
obs0.2027 237404 76.8 %-
Displacement parametersBiso max: 116.14 Å2 / Biso mean: 38.32 Å2 / Biso min: 12.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.6072 Å20 Å2-0.5759 Å2
2---0.3589 Å20 Å2
3----0.2482 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.964→188.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25877 0 458 2523 28858
Biso mean--54.3 45.06 -
Num. residues----3412
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9672SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4913HARMONIC5
X-RAY DIFFRACTIONt_it27032HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3607SEMIHARMONIC5
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_contact25917SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d27185HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg37026HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion15.88
LS refinement shellResolution: 1.964→2.08 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3163 218 4.59 %
Rwork0.2752 4531 -

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