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- PDB-5sdt: Structure of liver pyruvate kinase in complex with anthraquinone ... -

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Basic information

Entry
Database: PDB / ID: 5sdt
TitleStructure of liver pyruvate kinase in complex with anthraquinone derivative 15
ComponentsPyruvate kinase
KeywordsTRANSFERASE/TRANSFERASE inhibitor / Pyruvate kinase / active site / inhibition / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / cellular response to insulin stimulus / kinase activity / magnesium ion binding / ATP binding / cytoplasm
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 / Chem-I9Q / : / OXALATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.944 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 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)392,56346
Polymers386,2838
Non-polymers6,28038
Water47,2352622
1
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,28223
Polymers193,1424
Non-polymers3,14019
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21810 Å2
ΔGint-139 kcal/mol
Surface area56780 Å2
MethodPISA
2
E: Pyruvate kinase
F: Pyruvate kinase
G: Pyruvate kinase
H: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,28223
Polymers193,1424
Non-polymers3,14019
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22620 Å2
ΔGint-135 kcal/mol
Surface area56540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.459, 112.335, 188.148
Angle α, β, γ (deg.)90.000, 91.710, 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


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) / References: UniProt: Q16716, 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, 2652 molecules

#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-I9Q / N-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracene-2-sulfonyl)-beta-alanine


Mass: 391.352 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H13NO8S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2622 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.945→188.064 Å / Num. obs: 252169 / % possible obs: 85.5 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Net I/σ(I): 13.3 / Num. measured all: 1755052
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsCC1/2Rpim(I) all
1.945-2.03854.47.41.2991.593201126080.6390.512
5.735-188.06499.97.20.02843.9905281260710.011

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
PHASERphasing
BUSTER2.10.4 (16-JUL-2021)refinement
PDB_EXTRACT3.25data extraction
STARANISOdata scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 1.944→188.06 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.159
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
Rfree0.2229 12521 4.96 %RANDOM
Rwork0.1966 ---
obs0.1978 252205 79.7 %-
Displacement parametersBiso max: 125.84 Å2 / Biso mean: 40.25 Å2 / Biso min: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.4107 Å20 Å2-0.2492 Å2
2---0.0518 Å20 Å2
3----0.3589 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.944→188.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25949 0 386 2626 28961
Biso mean--44.69 48.83 -
Num. residues----3418
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9788SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4958HARMONIC5
X-RAY DIFFRACTIONt_it27235HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3659SEMIHARMONIC5
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_contact26190SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d27313HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg37163HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion16.01
LS refinement shellResolution: 1.94→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2978 237 4.7 %
Rwork0.2708 4808 -
all0.272 5045 -
obs--19.39 %

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