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- PDB-4mta: Crystal structure of Pim-1 kinase domain in complex with 2-methyl... -

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Basic information

Entry
Database: PDB / ID: 4mta
TitleCrystal structure of Pim-1 kinase domain in complex with 2-methyl-5-phenylfuran-3-carboxylic acid
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / Serine/threonine-protein kinase / ATP-binding
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / 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 / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / 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 / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / 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 / protein stabilization / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / Protein kinase, ATP binding site ...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
2-methyl-5-phenylfuran-3-carboxylic acid / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsScheufler, C. / Be, C.
CitationJournal: J Biomol Screen / Year: 2015
Title: Large scale meta-analysis of fragment-based screening campaigns: privileged fragments and complementary technologies.
Authors: Kutchukian, P.S. / Wassermann, A.M. / Lindvall, M.K. / Wright, S.K. / Ottl, J. / Jacob, J. / Scheufler, C. / Marzinzik, A. / Brooijmans, N. / Glick, M.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Serine/threonine-protein kinase pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1413
Polymers32,8461
Non-polymers2942
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.790, 95.790, 79.760
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 Serine/threonine-protein kinase pim-1


Mass: 32846.285 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 119-404)
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-2D2 / 2-methyl-5-phenylfuran-3-carboxylic acid


Mass: 202.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.0 M ammonium dihydrogen phosphate, 0.2 M sodium chloride, 0.1 M sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9919 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 21227 / Num. obs: 21108 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.116 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 3.75 % / Mean I/σ(I) obs: 3.72 / Rsym value: 0.534 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.4refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XR1

1xr1


Resolution: 2.2→23.95 Å / Cor.coef. Fo:Fc: 0.9513 / Cor.coef. Fo:Fc free: 0.9305 / SU R Cruickshank DPI: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.161 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1056 5 %RANDOM
Rwork0.1584 ---
obs0.16 21106 99.52 %-
Displacement parametersBiso mean: 38.94 Å2
Baniso -1Baniso -2Baniso -3
1--3.3463 Å20 Å20 Å2
2---3.3463 Å20 Å2
3---6.6927 Å2
Refine analyzeLuzzati coordinate error obs: 0.231 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 21 167 2400
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092292HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.973110HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d788SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes334HARMONIC5
X-RAY DIFFRACTIONt_it2292HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion15.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
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_contact3068SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.31 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2232 141 5 %
Rwork0.1817 2680 -
all0.1839 2821 -
obs--99.52 %
Refinement TLS params.Method: refined / Origin x: 65.5927 Å / Origin y: 26.9531 Å / Origin z: -0.7452 Å
111213212223313233
T-0.0574 Å2-0.0286 Å2-0.0224 Å2--0.0516 Å2-0.0339 Å2---0.1038 Å2
L1.339 °20.0828 °2-0.2937 °2-1.1067 °2-0.3779 °2--1.9924 °2
S0.0108 Å °0.0476 Å °0.0723 Å °-0.0357 Å °0.0626 Å °-0.0454 Å °-0.0377 Å °0.2201 Å °-0.0733 Å °
Refinement TLS groupSelection details: { A|* }

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