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- PDB-2xiy: Protein kinase Pim-1 in complex with fragment-2 from crystallogra... -

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Basic information

Entry
Database: PDB / ID: 2xiy
TitleProtein kinase Pim-1 in complex with fragment-2 from crystallographic fragment screen
ComponentsPROTO-ONCOGENE SERINE/THREONINE PROTEIN KINASE PIM-1
KeywordsTRANSFERASE / PHOSPHORYLATION
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter 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 cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter 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 / negative regulation of DNA-binding transcription factor 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 mitotic cell cycle / negative regulation of innate immune response / protein serine/threonine kinase activator activity / cellular response to type II interferon / manganese ion binding / protein autophosphorylation / Interleukin-4 and Interleukin-13 signaling / protein phosphorylation / non-specific serine/threonine protein kinase / protein stabilization / 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 / cytoplasm / cytosol
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
2-HYDROXYMETHYL-BENZOIMIDAZOLE / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchulz, M.N. / Fanghanel, J. / Schafer, M. / Badock, V. / Briem, H. / Boemer, U. / Nguyen, D. / Husemann, M. / Hillig, R.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Crystallographic Fragment Screen Identifies Cinnamic Acid Derivatives as Starting Points for Potent Pim-1 Inhibitors
Authors: Schulz, M.N. / Fanghanel, J. / Schafer, M. / Badock, V. / Briem, H. / Boemer, U. / Nguyen, D. / Husemann, M. / Hillig, R.C.
History
DepositionJul 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)34,7435
Polymers34,3891
Non-polymers3544
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.987, 96.987, 80.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTO-ONCOGENE SERINE/THREONINE PROTEIN KINASE PIM-1


Mass: 34388.934 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 14-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30A, HIS-TEV-PIM-1(14-313) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P11309, EC: 2.7.1.37, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 136 molecules

#2: Chemical ChemComp-XIY / 2-HYDROXYMETHYL-BENZOIMIDAZOLE / 1H-BENZIMIDAZOL-2-YLMETHANOL


Mass: 148.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsGLYCEROL (GOL): ARTIFACT FROM CRYO BUFFER CHLORIDE ION (CL): ARTIFACT FROM CRYSTALLIZATION BUFFER ...GLYCEROL (GOL): ARTIFACT FROM CRYO BUFFER CHLORIDE ION (CL): ARTIFACT FROM CRYSTALLIZATION BUFFER DIMETHYLSULFOXIDE (DMS): ARTIFACT FROM SOAKING PROCEDURE
Sequence detailsN-TERMINAL GLY FROM TEV CLEAVAGE SITE

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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: 3.28 Å3/Da / Density % sol: 62.8 % / Description: SOLVED BY RIGID BODY REFINEMENT
Crystal growpH: 5.5
Details: 0.9 M (NH4)2HPO4,0.1 M SODIUM CITRATE PH=5.5 , 0.2M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: May 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→48.6 Å / Num. obs: 21175 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.25 / % possible all: 71.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE PIM-1 STRUCTURE

Resolution: 2.2→48.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.666 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20075 1065 5 %RANDOM
Rwork0.16994 ---
obs0.1715 20074 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.238 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0.25 Å20 Å2
2---0.5 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 22 132 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.9593230
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81823.04125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98515.038399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.421524
X-RAY DIFFRACTIONr_chiral_restr0.080.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021852
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.21079
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21573
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.90421447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.81532267
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7094.51076
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3816958
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 46 -
Rwork0.218 1081 -
obs--69.35 %
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)
110.2918-2.0364-1.88523.52961.52595.4265-0.007-0.7125-0.1320.24660.0844-0.24510.08190.5816-0.07730.01580.0744-0.06980.1496-0.0128-0.2683-16.526-33.4817.55
22.02970.45110.74082.4023-0.13463.0646-0.02810.0228-0.0609-0.09190.1264-0.11850.03790.0869-0.0983-0.09290.02970.0472-0.082-0.0214-0.3613-37.085-24.543-3.468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 123
2X-RAY DIFFRACTION2A124 - 306

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