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- PDB-2o3p: Crystal structure of Pim1 with Quercetin -

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Basic information

Entry
Database: PDB / ID: 2o3p
TitleCrystal structure of Pim1 with Quercetin
ComponentsProto-oncogene serine/threonine-protein kinase Pim-1
KeywordsTRANSFERASE / Pim1 / Quercetin
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / positive regulation of TORC1 signaling / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase pim-1/2/3 / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsHolder, S. / Zemskova, M. / Zhang, C. / Tabrizizad, M. / Bremer, R. / Neidigh, J.W. / Lilly, M.B.
CitationJournal: Mol.Cancer Ther. / Year: 2007
Title: Characterization of a potent and selective small-molecule inhibitor of the PIM1 kinase.
Authors: Holder, S. / Zemskova, M. / Zhang, C. / Tabrizizad, M. / Bremer, R. / Neidigh, J.W. / Lilly, M.B.
History
DepositionDec 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Proto-oncogene serine/threonine-protein kinase Pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2734
Polymers33,8321
Non-polymers4403
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.761, 97.761, 81.185
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Proto-oncogene serine/threonine-protein kinase Pim-1


Mass: 33832.320 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NA ACETATE, IMIDAZOLE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.24→84.51 Å / Num. all: 22140 / Num. obs: 22140 / % possible obs: 99.18 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 24.19 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 8.5
Reflection shellResolution: 2.24→2.298 Å / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 1.4 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
Blu-Icedata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→84.51 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.122 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.205 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22019 1083 5.1 %RANDOM
Rwork0.18701 ---
all0.18866 20049 --
obs0.18866 20049 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.188 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20.83 Å20 Å2
2--1.66 Å20 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.174 Å0.205 Å
Refinement stepCycle: LAST / Resolution: 2.24→84.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 54 111 2403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212358
X-RAY DIFFRACTIONr_bond_other_d0.0020.022095
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.973205
X-RAY DIFFRACTIONr_angle_other_deg0.80534848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9275275
X-RAY DIFFRACTIONr_chiral_restr0.0840.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022632
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02520
X-RAY DIFFRACTIONr_nbd_refined0.1970.2465
X-RAY DIFFRACTIONr_nbd_other0.2350.22443
X-RAY DIFFRACTIONr_nbtor_other0.0810.21387
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.25
X-RAY DIFFRACTIONr_mcbond_it0.5531.51371
X-RAY DIFFRACTIONr_mcangle_it1.08222223
X-RAY DIFFRACTIONr_scbond_it1.5673987
X-RAY DIFFRACTIONr_scangle_it2.6874.5982
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 74 -
Rwork0.264 1397 -
obs-1397 96.8 %
Refinement TLS params.Method: refined / Origin x: 66.859 Å / Origin y: 27.515 Å / Origin z: -0.83 Å
111213212223313233
T0.0485 Å2-0.029 Å2-0.0336 Å2-0.0711 Å2-0.024 Å2--0.1028 Å2
L2.4551 °20.2916 °2-0.5182 °2-1.8141 °2-0.1018 °2--1.6595 °2
S-0.0662 Å °0.0938 Å °0.1024 Å °-0.0406 Å °0.0669 Å °-0.1715 Å °-0.0603 Å °0.1907 Å °-0.0007 Å °

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