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- PDB-4gw8: Human proto-oncogene serine threonine kinase (PIM1) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4gw8
TitleHuman proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and Leucettine L41
Components
  • Consensus peptide (Pimtide)
  • Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / ONCOGENE / KINASE / SERINE-THREONINE / PIM1 / STRUCTURAL GENOMICS CONSORTIUM / SGC / ALTERNATIVE INITIATION / ATP-BINDING / MANGANESE / MEMBRANE / METAL-BINDING / NUCLEOTIDE-BINDING / NUCLEUS / PHOSPHOPROTEIN / PROTO-ONCOGENE / SERINE/THREONINE-PROTEIN KINASE / HOST-VIRUS INTERACTION / VIRAL IMMUNOEVASION / VIRION / VIRULENCE / CELL CYCLE / CELL MEMBRANE
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 / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / 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 / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / 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
Chem-3RA / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsFilippakopoulos, P. / Bullock, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Meijer, L. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2012
Title: Selectivity, cocrystal structures, and neuroprotective properties of leucettines, a family of protein kinase inhibitors derived from the marine sponge alkaloid leucettamine B.
Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A.E. / Pearl, L.H. / ...Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A.E. / Pearl, L.H. / Carreaux, F. / Bazureau, J.P. / Knapp, S. / Meijer, L.
History
DepositionSep 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase pim-1
B: Consensus peptide (Pimtide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5534
Polymers37,1832
Non-polymers3692
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint4 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.006, 98.006, 80.497
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / Fragment: Isoform 2 / Mutation: R250G
Source method: isolated from a genetically manipulated source
Details: THE EXPRESSED PROTEIN HAS THE SEQUENCE FROM GI33304198 WHICH DIFFERS FROM GI 4505811 BY A SINGLE MUTATION R250G
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Protein/peptide Consensus peptide (Pimtide)


Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic consensus peptide (Pimtide)
#3: Chemical ChemComp-3RA / 5-(1,3-benzodioxol-5-ylmethyl)-2-(phenylamino)-4H-imidazol-4-one


Mass: 307.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13N3O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16M Na(OAc), 0.08M BTProp pH 8.5 , 16% PEG3350, 8% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 6.3 % / Av σ(I) over netI: 9.7 / Number: 180841 / Rsym value: 0.074 / D res high: 1.9 Å / D res low: 19.582 Å / Num. obs: 28862 / % possible obs: 97
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.3219.5896.210.0230.0236
4.476.3299.510.0250.0256.3
3.654.4799.110.030.036.3
3.163.6598.410.0450.0456.3
2.833.1698.110.0830.0836.3
2.582.8397.610.1450.1456.3
2.392.5896.910.2290.2296.3
2.242.3996.410.3310.3316.3
2.112.2495.510.5780.5786.3
22.1194.910.910.916.2
ReflectionResolution: 2→19.582 Å / Num. all: 29755 / Num. obs: 28862 / % possible obs: 97 % / Redundancy: 6.3 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.116.20.910.92568241140.9194.9
2.11-2.246.30.5781.32448139100.57895.5
2.24-2.396.30.3312.32326237090.33196.4
2.39-2.586.30.2293.32191234850.22996.9
2.58-2.836.30.1455.32019132120.14597.6
2.83-3.166.30.08391849029420.08398.1
3.16-3.656.30.04516.21636825980.04598.4
3.65-4.476.30.0322.61403122310.0399.1
4.47-6.326.30.025251082817280.02599.5
6.32-19.58260.02325.955969330.02396.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.58 Å
Translation2.5 Å19.58 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.2data scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C3I

2c3i


Resolution: 2→19.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2218 / WRfactor Rwork: 0.1977 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8844 / SU B: 6.932 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1725 / SU Rfree: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1456 5 %RANDOM
Rwork0.1758 ---
all0.1776 29708 --
obs0.1776 28852 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.14 Å2 / Biso mean: 36.226 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 27 198 2509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212410
X-RAY DIFFRACTIONr_bond_other_d0.0010.021686
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9713266
X-RAY DIFFRACTIONr_angle_other_deg0.9353.0024020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56322.623122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21915391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5921525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
X-RAY DIFFRACTIONr_mcbond_it3.39231403
X-RAY DIFFRACTIONr_mcbond_other1.1453571
X-RAY DIFFRACTIONr_mcangle_it4.53152269
X-RAY DIFFRACTIONr_scbond_it7.72881007
X-RAY DIFFRACTIONr_scangle_it9.30311997
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 114 -
Rwork0.33 1923 -
all-2037 -
obs--94.66 %
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)
12.6789-0.7661-0.667610.00821.9693.9245-0.1725-0.45760.12770.29830.14241.49970.0569-0.54590.03010.1184-0.0555-0.06210.37210.05560.383-28.520833.69925.0156
23.99652.91150.89968.6106-1.91314.23040.2436-0.3465-0.32610.5938-0.1878-0.12190.47130.1216-0.05580.1716-0.02520.00480.20060.03380.0903-16.745129.543711.135
31.79990.045-0.12792.1832-0.55772.37860.082-0.085-0.0484-0.1102-0.0240.04590.03160.0593-0.0580.0123-0.0068-0.00720.04220.00240.0055-2.883644.79-1.7755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 64
2X-RAY DIFFRACTION2A65 - 121
3X-RAY DIFFRACTION3A122 - 305

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