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- PDB-4g1n: PKM2 in complex with an activator -

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Basic information

Entry
Database: PDB / ID: 4g1n
TitlePKM2 in complex with an activator
ComponentsPyruvate kinase isozymes M1/M2
KeywordsTransferase/Activator / pyruvate kinase / aerobic glycolysis / activator / cancer metabolism / phosphorylation of pyruvate / Transferase-Activator complex
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / programmed cell death / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / programmed cell death / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / protein tyrosine kinase activity / secretory granule lumen / collagen-containing extracellular matrix / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / phosphorylation / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / 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 / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-NZT / OXALATE ION / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKung, C. / Hixon, J. / Dang, L. / DeLaBarre, B. / Qian, K.C.
CitationJournal: Chem.Biol. / Year: 2012
Title: Small Molecule Activation of PKM2 in Cancer Cells Induces Serine Auxotrophy.
Authors: Kung, C. / Hixon, J. / Choe, S. / Marks, K. / Gross, S. / Murphy, E. / Delabarre, B. / Cianchetta, G. / Sethumadhavan, S. / Wang, X. / Yan, S. / Gao, Y. / Fang, C. / Wei, W. / Jiang, F. / ...Authors: Kung, C. / Hixon, J. / Choe, S. / Marks, K. / Gross, S. / Murphy, E. / Delabarre, B. / Cianchetta, G. / Sethumadhavan, S. / Wang, X. / Yan, S. / Gao, Y. / Fang, C. / Wei, W. / Jiang, F. / Wang, S. / Qian, K. / Saunders, J. / Driggers, E. / Woo, H.K. / Kunii, K. / Murray, S. / Yang, H. / Yen, K. / Liu, W. / Cantley, L.C. / Vander Heiden, M.G. / Su, S.M. / Jin, S. / Salituro, F.G. / Dang, L.
History
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase isozymes M1/M2
B: Pyruvate kinase isozymes M1/M2
C: Pyruvate kinase isozymes M1/M2
D: Pyruvate kinase isozymes M1/M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,02814
Polymers226,6294
Non-polymers1,39810
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19270 Å2
ΔGint-121 kcal/mol
Surface area72670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.118, 94.141, 146.149
Angle α, β, γ (deg.)90.000, 99.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-721-

HOH

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Components

#1: Protein
Pyruvate kinase isozymes M1/M2 / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate kinase 2/3 / Pyruvate kinase muscle isozyme / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / p58


Mass: 56657.289 Da / Num. of mol.: 4 / Fragment: UNP residues 14-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM2, OIP3, PK2, PK3, PKM / Production host: Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase
#2: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NZT / N-(4-{[4-(pyrazin-2-yl)piperazin-1-yl]carbonyl}phenyl)quinoline-8-sulfonamide


Mass: 474.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22N6O3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.8
Details: 0.1 M Imidazole pH 7.8, 20 %(w/v) PEG 6000, 15 mg/ml PKM2, EVAPORATION, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 94346 / Num. obs: 94063 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.24 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.44 / SU B: 8.43 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R: 0.37 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 4951 5 %RANDOM
Rwork0.2115 ---
all0.2142 ---
obs-94063 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 181.22 Å2 / Biso mean: 48.2193 Å2 / Biso min: 19.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.02 Å2
2--0.32 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15860 0 96 222 16178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916271
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.97921989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52852074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01623.931669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24152929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.51515125
X-RAY DIFFRACTIONr_chiral_restr0.0850.22514
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112105
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 399 -
Rwork0.279 6859 -
all-7258 -
obs--98.59 %

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