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- PDB-1yxx: Crystal Structure of Kinase Pim1 in complex with (3E)-3-[(4-HYDRO... -

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Basic information

Entry
Database: PDB / ID: 1yxx
TitleCrystal Structure of Kinase Pim1 in complex with (3E)-3-[(4-HYDROXYPHENYL)IMINO]-1H-INDOL-2(3H)-ONE
ComponentsProto-oncogene serine/threonine-protein kinase Pim-1
KeywordsTRANSFERASE / Ser/Thr protein kinase
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 / protein serine/threonine kinase activator activity / positive regulation of brown fat cell differentiation / negative regulation of innate immune response / 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
IMIDAZOLE / Chem-LI7 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKumar, A. / Mandiyan, V. / Suzuki, Y. / Zhang, C. / Rice, J. / Tsai, J. / Artis, D.R. / Ibrahim, P. / Bremer, R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of proto-oncogene kinase Pim1: a target of aberrant somatic hypermutations in diffuse large cell lymphoma.
Authors: Kumar, A. / Mandiyan, V. / Suzuki, Y. / Zhang, C. / Rice, J. / Tsai, J. / Artis, D.R. / Ibrahim, P. / Bremer, R.
History
DepositionFeb 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jun 24, 2015Group: Data collection
Revision 1.4Feb 14, 2024Group: 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)34,1403
Polymers33,8321
Non-polymers3072
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.592, 96.592, 80.556
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, EC: 2.7.1.37
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-LI7 / (3E)-3-[(4-HYDROXYPHENYL)IMINO]-1H-INDOL-2(3H)-ONE


Mass: 238.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.8 Å3/Da / Density % sol: 67 %
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
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.96→83.7 Å / Num. obs: 29990 / % possible obs: 97.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 8.9
Reflection shellResolution: 1.96→2.07 Å / % possible obs: 96.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / Num. measured obs: 4338 / Rsym value: 0.369 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.1.25refinement
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→83.65 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.37 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R: 0.159 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1459 5 %RANDOM
Rwork0.218 ---
all0.219 0 --
obs0.218 27652 97.61 %-
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: 28.056 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.6 Å20 Å2
2--1.21 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2→83.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 23 105 2358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212325
X-RAY DIFFRACTIONr_bond_other_d0.0020.022089
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9533156
X-RAY DIFFRACTIONr_angle_other_deg0.82634836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0895275
X-RAY DIFFRACTIONr_chiral_restr0.0850.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022599
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02514
X-RAY DIFFRACTIONr_nbd_refined0.2020.2490
X-RAY DIFFRACTIONr_nbd_other0.2350.22465
X-RAY DIFFRACTIONr_nbtor_other0.080.21401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.28
X-RAY DIFFRACTIONr_mcbond_it0.5941.51371
X-RAY DIFFRACTIONr_mcangle_it1.07622223
X-RAY DIFFRACTIONr_scbond_it1.6013954
X-RAY DIFFRACTIONr_scangle_it2.6254.5933
LS refinement shellResolution: 2→2.031 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 112
Rwork0.315 2028
Refinement TLS params.Method: refined / Origin x: 66.19 Å / Origin y: 27.372 Å / Origin z: -0.83 Å
111213212223313233
T0.0589 Å2-0.0187 Å2-0.0198 Å2-0.0682 Å2-0.0269 Å2--0.0269 Å2
L1.8695 °20.2065 °2-0.2202 °2-1.9151 °2-0.2247 °2--1.7637 °2
S0.0007 Å °0.063 Å °0.1135 Å °-0.0956 Å °0.0674 Å °-0.1036 Å °-0.0668 Å °0.2548 Å °-0.0681 Å °
Refinement TLS groupSelection: ALL

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