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- PDB-4b2d: human PKM2 with L-serine and FBP bound. -

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Basic information

Entry
Database: PDB / ID: 4b2d
Titlehuman PKM2 with L-serine and FBP bound.
Components(PYRUVATE KINASE ISOZYMES ...) x 2
KeywordsTRANSFERASE / TUMOUR / PKM2 / GLYCOLYSIS
Function / homology
Function and homology information


positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / 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 / cytoplasm / cytosol
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
1,6-di-O-phosphono-beta-D-fructofuranose / SERINE / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChaneton, B. / Hillmann, P. / Zheng, L. / Martin, A.C.L. / Maddocks, O.D.K. / Chokkathukalam, A. / Coyle, J.E. / Jankevics, A. / Holding, F.P. / Vousden, K.H. ...Chaneton, B. / Hillmann, P. / Zheng, L. / Martin, A.C.L. / Maddocks, O.D.K. / Chokkathukalam, A. / Coyle, J.E. / Jankevics, A. / Holding, F.P. / Vousden, K.H. / Frezza, C. / O'Reilly, M. / Gottlieb, E.
CitationJournal: Nature / Year: 2012
Title: Serine is a natural ligand and allosteric activator of pyruvate kinase M2.
Authors: Chaneton, B. / Hillmann, P. / Zheng, L. / Martin, A.C.L. / Maddocks, O.D.K. / Chokkathukalam, A. / Coyle, J.E. / Jankevics, A. / Holding, F.P. / Vousden, K.H. / Frezza, C. / O'Reilly, M. / Gottlieb, E.
History
DepositionJul 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Feb 6, 2013Group: Atomic model / Derived calculations / Other
Revision 1.4Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_id_ISSN ..._audit_author.name / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_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_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)241,15714
Polymers239,3274
Non-polymers1,82910
Water22,3931243
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17950 Å2
ΔGint-100 kcal/mol
Surface area72060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.611, 151.098, 91.791
Angle α, β, γ (deg.)90.00, 102.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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PYRUVATE KINASE ISOZYMES ... , 2 types, 4 molecules ABCD

#1: Protein PYRUVATE KINASE ISOZYMES M1/M2 / PYRUVATE KINASE M2 / CYTOSOLIC THYROID HORMONE-BINDING PROTEIN CTHBP / OPA-INTERACTING PROTEIN 3 / ...PYRUVATE KINASE M2 / 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: 59831.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14618, pyruvate kinase
#2: Protein PYRUVATE KINASE ISOZYMES M1/M2 / PYRUVATE KINASE M2 / CYTOSOLIC THYROID HORMONE-BINDING PROTEIN CTHBP / OPA-INTERACTING PROTEIN 3 / ...PYRUVATE KINASE M2 / 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: 59831.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14618, pyruvate kinase

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Sugars , 1 types, 4 molecules

#4: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 1249 molecules

#3: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1243 / 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: 2.28 Å3/Da / Density % sol: 46.16 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN SOLUTION 10 MG/ML, 25 MM TRIS/HCL PH 7.5, 0.1 M KCL, 5 MM MGCL2, 10% (V/V) GLYCEROL WAS MIXED IN A (1:1) RATIO WITH RESERVOIR SOLUTION CONTAINING 0.1 M KCL, 0.2 M AMMONIUM TARTRATE, 24% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→89.78 Å / Num. obs: 93236 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.6 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
CSEARCHphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H6O

3h6o


Resolution: 2.3→78.85 Å / Cor.coef. Fo:Fc: 0.9387 / Cor.coef. Fo:Fc free: 0.9129 / SU R Cruickshank DPI: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.342 / SU Rfree Blow DPI: 0.22 / SU Rfree Cruickshank DPI: 0.221
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 4702 5.05 %RANDOM
Rwork0.1735 ---
obs0.1762 93185 97.91 %-
Displacement parametersBiso mean: 58.69 Å2
Baniso -1Baniso -2Baniso -3
1-8.1671 Å20 Å212.2442 Å2
2---7.3352 Å20 Å2
3----0.8318 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: LAST / Resolution: 2.3→78.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15595 0 110 1243 16948
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01215986HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0921668HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5639SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes362HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2435HARMONIC5
X-RAY DIFFRACTIONt_it15986HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.88
X-RAY DIFFRACTIONt_other_torsion18.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2188SEMIHARMONIC5
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_contact20065SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2792 342 4.98 %
Rwork0.2255 6521 -
all0.2281 6863 -
obs--97.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.55690.8374-0.0260.84360.0860.65810.13980.2699-0.2798-0.2253-0.02530.08870.1163-0.0005-0.1145-0.08830.0744-0.0879-0.0151-0.0415-0.0158-10.84351.1122-3.0674
25.94373.1427-2.77798.3154-2.3074.74680.11110.08630.636-0.26780.1896-0.0426-0.4525-0.2844-0.3007-0.22570.10040.0253-0.23220.11040.1675-14.658636.14783.2208
31.9236-0.0140.04640.71590.04110.67310.11890.09760.01-0.0402-0.03830.11140.0269-0.0465-0.0806-0.13340.0385-0.0352-0.00730.05020.0323-11.021810.66517.0508
41.5392-0.49060.65782.3189-0.92791.37850.12250.146-0.2272-0.1339-0.08140.27120.18660.0776-0.0412-0.09840.0246-0.0872-0.1264-0.03620.1142-11.0214-14.66649.8698
53.12390.4394-0.24471.0286-0.1950.95620.21330.45530.5240.0385-0.1429-0.1887-0.23810.1125-0.0704-0.2580.06170.0286-0.06710.16290.031218.347925.9823.7271
61.6922-1.52882.51080.60072.59724.7239-0.11840.36940.1144-0.16110.1519-0.08230.2121-0.2115-0.03350.034-0.1628-0.09510.3040.1138-0.285912.09697.7072-29.0475
71.63170.3997-0.28021.140.05760.61550.03270.52270.0443-0.1979-0.0344-0.20520.08740.15830.0017-0.2130.09880.03880.14160.1054-0.025119.638414.5916-4.0154
82.64920.34780.63731.3965-0.34091.68710.09030.12020.31920.0835-0.0025-0.1641-0.10160.2389-0.0879-0.1910.00970.0017-0.0420.02320.092431.171919.104318.1173
91.75970.12760.50091.67110.25780.83510.0057-0.2154-0.2143-0.0398-0.00240.5480.1645-0.0152-0.0033-0.0580.0214-0.0703-0.16020.02980.070110.6005-35.955539.6262
103.07220.26430.16144.38010.78287.116-0.00130.2265-0.2296-0.21080.0885-0.52530.19580.6046-0.0872-0.18070.10480.0235-0.03750.0073-0.000946.0426-43.818539.6795
111.45760.27120.15212.32750.10730.75150.02520.1258-0.1669-0.25330.00620.09330.14190.1414-0.03140.0160.0312-0.1184-0.1332-0.0195-0.04122.2051-34.994332.2174
122.195-0.3910.67061.1613-0.24781.36520.0837-0.011-0.16130.1211-0.12360.17550.0604-0.11930.04-0.05790.0123-0.1295-0.1842-0.04080.1365-1.6752-29.631724.6565
131.99950.26220.87732.49670.23151.8156-0.0333-0.20310.15820.4673-0.049-0.37650.0280.09460.0824-0.0718-0.0215-0.1738-0.20650.0027-0.038539.6012-10.769946.5846
14-0.10253.0214-0.27074.0878-0.33424.8104-0.0883-0.1871-0.07590.11180.01230.00870.170.17690.0760.1154-0.147-0.03-0.1558-0.03920.008714.4334-22.39972.4863
151.62210.15580.2682.15670.42251.2694-0.0448-0.41320.22510.539-0.05840.0821-0.0384-0.07060.10320.0744-0.0288-0.1267-0.1495-0.0581-0.103926.9688-9.530152.0628
161.97420.32150.75022.7549-0.39210.94660.21060.0915-0.08650.3588-0.0144-0.43890.12650.1228-0.1962-0.06660.0062-0.1679-0.1683-0.03680.106238.0636.167835.495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESIDUES 14-116
2X-RAY DIFFRACTION2CHAIN A AND RESIDUES 117-218
3X-RAY DIFFRACTION3CHAIN A AND RESIDUES 219-389
4X-RAY DIFFRACTION4CHAIN A AND RESIDUES 390-700
5X-RAY DIFFRACTION5CHAIN B AND RESIDUES 14-116
6X-RAY DIFFRACTION6CHAIN B AND RESIDUES 117-218
7X-RAY DIFFRACTION7CHAIN B AND RESIDUES 219-389
8X-RAY DIFFRACTION8CHAIN B AND RESIDUES 390-600
9X-RAY DIFFRACTION9CHAIN C AND RESIDUES 14-116
10X-RAY DIFFRACTION10CHAIN C AND RESIDUES 117-218
11X-RAY DIFFRACTION11CHAIN C AND RESIDUES 219-389
12X-RAY DIFFRACTION12CHAIN C AND RESIDUES 390-700
13X-RAY DIFFRACTION13CHAIN D AND RESIDUES 14-116
14X-RAY DIFFRACTION14CHAIN D AND RESIDUES 117-218
15X-RAY DIFFRACTION15CHAIN D AND RESIDUES 219-389
16X-RAY DIFFRACTION16CHAIN D AND RESIDUES 390-600

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