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- PDB-6qxk: Human PIM1 bound to OX0999 -

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Basic information

Entry
Database: PDB / ID: 6qxk
TitleHuman PIM1 bound to OX0999
Components
  • Pimtide
  • Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / Kinase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / 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 protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation ...positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / 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 protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / regulation of transmembrane transporter activity / negative regulation of innate immune response / regulation of mitotic cell cycle / protein serine/threonine kinase activator activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / protein autophosphorylation / Interleukin-4 and Interleukin-13 signaling / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Chem-JKW / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAlexander, L.T. / Elkins, J.M. / Russell, A. / Bountra, C. / Edwards, A.M. / Knapp, S.
CitationJournal: To Be Published
Title: PIM1 bound to OX0999
Authors: Knapp, S. / Elkins, J.M. / Alexander, L.T. / Russell, A.
History
DepositionMar 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Serine/threonine-protein kinase pim-1
A: Pimtide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6683
Polymers37,1832
Non-polymers4851
Water2,414134
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint4 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.889, 97.889, 80.370
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: 35590.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pLIC-SGC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Protein/peptide Pimtide


Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical ChemComp-JKW / 2-[(1-methylpiperidin-4-yl)methylamino]-5-[[2-[4-(trifluoromethyloxy)phenyl]-1,3-thiazol-4-yl]methyl]-1,3-thiazol-4-one


Mass: 484.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23F3N4O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M NaNO3, 0.1M bis-tris propane pH 8.5, 20% PEG 3350, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.1→84.77 Å / Num. obs: 25672 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3737 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C3I

2c3i


Resolution: 2.1→84.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.794 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20081 1307 5.1 %RANDOM
Rwork0.17546 ---
obs0.17675 24330 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.469 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å2-0 Å2
3----3.39 Å2
Refinement stepCycle: 1 / Resolution: 2.1→84.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 32 134 2412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192347
X-RAY DIFFRACTIONr_bond_other_d0.0010.022134
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9423185
X-RAY DIFFRACTIONr_angle_other_deg0.9152.9854927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91922.727121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70415383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1671522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
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_it1.2092.8081107
X-RAY DIFFRACTIONr_mcbond_other1.192.8061106
X-RAY DIFFRACTIONr_mcangle_it2.0724.1951379
X-RAY DIFFRACTIONr_mcangle_other2.0714.1981380
X-RAY DIFFRACTIONr_scbond_it1.182.9691240
X-RAY DIFFRACTIONr_scbond_other1.182.9711241
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0394.41806
X-RAY DIFFRACTIONr_long_range_B_refined4.86632.5912608
X-RAY DIFFRACTIONr_long_range_B_other4.86532.6052609
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 100 -
Rwork0.267 1796 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 107.4261 Å / Origin y: 97.7535 Å / Origin z: -3.4588 Å
111213212223313233
T0.0323 Å2-0.0016 Å2-0.0056 Å2-0.0185 Å2-0.0074 Å2--0.0367 Å2
L1.2024 °2-0.3976 °20.4542 °2-3.137 °2-0.6707 °2--2.4494 °2
S0.0717 Å °0.0026 Å °-0.1818 Å °0.0154 Å °-0.0407 Å °-0.0475 Å °0.2466 Å °0.0748 Å °-0.031 Å °

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