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- PDB-3we8: Pim-1 kinase in complex with Ruthenium-based inhibitor -

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Basic information

Entry
Database: PDB / ID: 3we8
TitlePim-1 kinase in complex with Ruthenium-based inhibitor
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor 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 / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor 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 / positive regulation of brown fat cell differentiation / negative regulation of innate immune response / 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 / 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 / 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
Chem-RUI / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å
AuthorsWaehler, K. / Kraeling, K. / Steuber, H. / Meggers, E.
CitationJournal: ChemistryOpen / Year: 2013
Title: Non-ATP-Mimetic Organometallic Protein Kinase Inhibitor
Authors: Wahler, K. / Kraling, K. / Steuber, H. / Meggers, E.
History
DepositionJul 2, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 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_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: Serine/threonine-protein kinase pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8983
Polymers31,4181
Non-polymers4802
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.730, 97.730, 81.190
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: 31417.654 Da / Num. of mol.: 1 / Fragment: UNP residues 124-396 / Mutation: R250G
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-RUI / Cyclopentadienyl(carbon monoxide)(7-oxo-7,10-dihydro-1,8-phenanthrolin-10-yl-kappa~2~C~10~,N~1~)ruthenium


Mass: 384.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H7N2O2Ru
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Bis-Tris Propan, 200mM Li-sulphate, 12% PEG 3350, 10% EG, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 15, 2012
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 31990 / Num. obs: 31990 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.1 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 6166 / Rsym value: 0.643 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XWS

1xws


Resolution: 1.954→42.318 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.8978 / SU ML: 0.1 / σ(F): 2 / Phase error: 17.43 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1773 960 3 %random
Rwork0.1513 ---
all0.16 31990 --
obs0.1522 31990 99.98 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.53 Å2 / Biso mean: 30.935 Å2 / Biso min: 8.27 Å2
Refinement stepCycle: LAST / Resolution: 1.954→42.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 28 285 2530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152366
X-RAY DIFFRACTIONf_angle_d1.5533249
X-RAY DIFFRACTIONf_dihedral_angle_d13.671884
X-RAY DIFFRACTIONf_chiral_restr0.114341
X-RAY DIFFRACTIONf_plane_restr0.007415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.954-2.0570.25091360.209943944530
2.057-2.18590.18781370.176244224559
2.1859-2.35460.17671360.159244024538
2.3546-2.59150.21321370.15744294566
2.5915-2.96650.18911370.155144314568
2.9665-3.73710.1571370.137444424579
3.7371-42.32820.15561380.137144954633
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)
10.69630.0906-0.32850.392-0.01130.64950.02290.23170.164-0.11910.041-0.11640.00420.2530.0010.1611-0.0613-0.00070.2425-0.01460.2049-65.6178118.1732-8.8487
20.6993-0.0338-0.35680.82320.11721.1478-0.02780.00240.04580.08150.09890.0280.05880.02390.0620.1301-0.0065-0.02660.0817-0.00740.1002-86.2942109.06432.2706
32.5566-0.4328-0.05425.42540.37854.63980.0773-0.05430.21950.15180.275-0.0066-0.1191-0.0329-0.22180.2228-0.11470.01180.3399-0.06680.3029-71.3425119.691.2568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 33:123A33 - 123
2X-RAY DIFFRACTION2chain A and resid 124:305A124 - 305
3X-RAY DIFFRACTION3chain A and resid 401A401

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