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- PDB-5np8: PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethy... -

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Basic information

Entry
Database: PDB / ID: 5np8
TitlePGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid)
ComponentsPhosphoglycerate kinase 1
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


negative regulation of pyruvate decarboxylation to acetyl-CoA / Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase [NAD(P)H] activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation ...negative regulation of pyruvate decarboxylation to acetyl-CoA / Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase [NAD(P)H] activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / non-specific serine/threonine protein kinase / mitochondrial matrix / membrane raft / protein serine/threonine kinase activity / extracellular space / extracellular exosome / ATP binding / membrane / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / Chem-93T / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTurnbull, A.P. / Bilsland, A.E. / Liu, Y. / Sumpton, D. / Stevenson, K. / Cairney, C.J. / Roffey, J. / Jenkinson, D. / Keith, W.N.
CitationJournal: Neoplasia / Year: 2019
Title: A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation.
Authors: Bilsland, A.E. / Liu, Y. / Turnbull, A. / Sumpton, D. / Stevenson, K. / Cairney, C.J. / Boyd, S.M. / Roffey, J. / Jenkinson, D. / Keith, W.N.
History
DepositionApr 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.title / _citation.year
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7016
Polymers44,9551
Non-polymers7465
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-6 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.870, 103.900, 50.650
Angle α, β, γ (deg.)90.00, 99.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoglycerate kinase 1 / Cell migration-inducing gene 10 protein / Primer recognition protein 2 / PRP 2


Mass: 44954.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGK1, PGKA, MIG10, OK/SW-cl.110 / Production host: Escherichia coli (E. coli) / References: UniProt: P00558, phosphoglycerate kinase
#2: Chemical ChemComp-93T / 3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid


Mass: 374.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16BrN3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.4-2.8M Sodium potassium phosphate, pH 7.4 - 8.2, 10mM DTT
PH range: 7.4 - 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 28225 / % possible obs: 98.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.358 / Num. unique obs: 4041 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZGV

2zgv


Resolution: 1.9→28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.538 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22183 1410 5 %RANDOM
Rwork0.16792 ---
obs0.17074 26787 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.778 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0 Å2-0.16 Å2
2--0.53 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.9→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 46 234 3247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193071
X-RAY DIFFRACTIONr_bond_other_d0.0010.022975
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.9864153
X-RAY DIFFRACTIONr_angle_other_deg0.9163.0016830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.52525.405111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5415517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7761511
X-RAY DIFFRACTIONr_chiral_restr0.1120.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02621
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3252.3251618
X-RAY DIFFRACTIONr_mcbond_other2.3232.3231617
X-RAY DIFFRACTIONr_mcangle_it3.3233.4732020
X-RAY DIFFRACTIONr_mcangle_other3.3243.4752021
X-RAY DIFFRACTIONr_scbond_it3.0022.6361453
X-RAY DIFFRACTIONr_scbond_other2.982.6331450
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4573.8272130
X-RAY DIFFRACTIONr_long_range_B_refined6.17419.493534
X-RAY DIFFRACTIONr_long_range_B_other6.17119.4893534
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 85 -
Rwork0.18 1928 -
obs--96.13 %

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