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- PDB-8tbt: Structure of human erythrocyte pyruvate kinase in complex with an... -

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Basic information

Entry
Database: PDB / ID: 8tbt
TitleStructure of human erythrocyte pyruvate kinase in complex with an allosteric activator Compound 2
ComponentsPyruvate kinase PKLR
KeywordsTRANSFERASE/ACTIVATOR / Erythrocyte pyruvate kinase / PKR / PKLR / Allosteric Activator / Glycolysis / TRANSFERASE / TRANSFERASE-ACTIVATOR complex
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 / cytosol / 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-I07 / : / : / PYRUVIC ACID / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsJin, L. / Padyana, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2024
Title: Structure-Based Design of AG-946, a Pyruvate Kinase Activator.
Authors: Liu, T. / Padyana, A.K. / Judd, E.T. / Jin, L. / Hammoudeh, D. / Kung, C. / Dang, L.
History
DepositionJun 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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)237,52522
Polymers234,6614
Non-polymers2,86418
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22740 Å2
ΔGint-110 kcal/mol
Surface area72090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.354, 174.038, 87.336
Angle α, β, γ (deg.)90.000, 94.291, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#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: 58665.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Red blood cell/liver isoform / Source: (gene. exp.) Homo sapiens (human) / Gene: PKLR, PK1, PKL / Production host: Escherichia coli (E. coli) / 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 / Fructose 1,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 375 molecules

#3: Chemical
ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-I07 / {6-[(3-methoxyphenyl)methyl]-4-methyl-5-oxo-5,6-dihydro-4H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-2-yl}(methyl)sulfaniumolate


Mass: 387.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 mM MnSO4, 50 mM MES/KOH pH 6.0, 11 %(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.34→33.77 Å / Num. obs: 92656 / % possible obs: 97.17 % / Redundancy: 3.7 % / Biso Wilson estimate: 45.28 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.6
Reflection shellResolution: 2.342→2.426 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 9114

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→33.77 Å / SU ML: 0.3151 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 4551 4.91 %
Rwork0.1979 88101 -
obs0.2007 92652 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.87 Å2
Refinement stepCycle: LAST / Resolution: 2.34→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15495 0 164 361 16020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008215958
X-RAY DIFFRACTIONf_angle_d0.986721657
X-RAY DIFFRACTIONf_chiral_restr0.05612506
X-RAY DIFFRACTIONf_plane_restr0.00562814
X-RAY DIFFRACTIONf_dihedral_angle_d23.44442293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.370.33541440.29452616X-RAY DIFFRACTION86.3
2.37-2.40.31411510.27483008X-RAY DIFFRACTION99.97
2.4-2.430.29241600.26813035X-RAY DIFFRACTION99.94
2.43-2.460.34351540.26192980X-RAY DIFFRACTION99.9
2.46-2.490.33091520.27293040X-RAY DIFFRACTION99.91
2.49-2.520.33591450.2572982X-RAY DIFFRACTION100
2.52-2.560.28651520.25633029X-RAY DIFFRACTION100
2.56-2.60.31861610.24093013X-RAY DIFFRACTION99.94
2.6-2.640.35261770.25562999X-RAY DIFFRACTION100
2.64-2.680.29521420.24012978X-RAY DIFFRACTION99.71
2.68-2.730.28881550.23653083X-RAY DIFFRACTION99.97
2.73-2.780.26441600.2232924X-RAY DIFFRACTION99.94
2.78-2.830.29841380.2323086X-RAY DIFFRACTION99.78
2.83-2.890.33781260.23222986X-RAY DIFFRACTION99.71
2.89-2.950.32611520.23593029X-RAY DIFFRACTION99.78
2.95-3.020.31981960.23172979X-RAY DIFFRACTION99.44
3.02-3.090.29051680.22142984X-RAY DIFFRACTION99.68
3.09-3.180.28181720.22132984X-RAY DIFFRACTION99.34
3.18-3.270.27461350.21843006X-RAY DIFFRACTION99.43
3.27-3.380.2861270.21743018X-RAY DIFFRACTION99.12
3.38-3.50.26571640.212966X-RAY DIFFRACTION97.81
3.5-3.640.23871750.19712944X-RAY DIFFRACTION97.5
3.64-3.80.26681570.18532871X-RAY DIFFRACTION96.04
3.8-40.21981350.18142946X-RAY DIFFRACTION97.16
4-4.250.21841410.16142866X-RAY DIFFRACTION94.56
4.25-4.580.19141420.15662749X-RAY DIFFRACTION91.17
4.58-5.040.19791370.15552741X-RAY DIFFRACTION89.83
5.04-5.770.22871560.18112811X-RAY DIFFRACTION93.07
5.77-7.250.20111480.17912931X-RAY DIFFRACTION96.28
7.25-33.770.2081290.14832517X-RAY DIFFRACTION81.82

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