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- PDB-2j2i: Crystal Structure of the humab PIM1 in complex with LY333531 -

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Basic information

Entry
Database: PDB / ID: 2j2i
TitleCrystal Structure of the humab PIM1 in complex with LY333531
ComponentsPROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / ALTERNATIVE INITIATION / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / METAL-BINDING / PROTO-ONCOGENE / KINASE / CANCER / LEUKEMIA / MANGANESE / NUCLEAR PROTEIN / PROTO- ONCOGENE / PHOSPHORYLATION
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-LY4 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDebreczeni, J.E. / Bullock, A.N. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Knapp, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2007
Title: A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases.
Authors: Fedorov, O. / Marsden, B. / Pogacic, V. / Rellos, P. / Muller, S. / Bullock, A.N. / Schwaller, J. / Sundstrom, M. / Knapp, S.
History
DepositionAug 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.7Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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
B: PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0683
Polymers35,5031
Non-polymers5652
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.157, 98.157, 80.366
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 / HUMAN PIM1


Mass: 35503.422 Da / Num. of mol.: 1 / Fragment: RESIDUES 92-403 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LY4 / (9R)-9-[(DIMETHYLAMINO)METHYL]-6,7,10,11-TETRAHYDRO-9H,18H-5,21:12,17-DIMETHENODIBENZO[E,K]PYRROLO[3,4-H][1,4,13]OXADIA ZACYCLOHEXADECINE-18,20-DIONE / LY333531


Mass: 468.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H28N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, ARG 341 TO GLY
Sequence detailsSEQADV 2BIK GLY B 250 UNP P11309 ARG 250 VARIANT

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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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NA2SO4, 0.1 M BIS-TRIS-PROPANE PH 7.5, 20% PEG3350, 10% ETHYLENE-GLYCOL, 0.5% DMSO, SITTING DROP, VAPOR DIFFUSION, 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 4, 2006 / Details: VARIMAX MIRRORS
RadiationMonochromator: VARIMAX MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25.09 Å / Num. obs: 34673 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 5.27 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.91 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.5 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BIK

2bik


Resolution: 1.9→85.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.924 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1765 5.1 %RANDOM
Rwork0.179 ---
obs0.18 32879 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→85.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 40 168 2391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212349
X-RAY DIFFRACTIONr_bond_other_d0.0010.021607
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9913203
X-RAY DIFFRACTIONr_angle_other_deg0.8823.0043821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50823.036112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66115368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9321519
X-RAY DIFFRACTIONr_chiral_restr0.080.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined0.2020.2425
X-RAY DIFFRACTIONr_nbd_other0.1850.21633
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21102
X-RAY DIFFRACTIONr_nbtor_other0.080.21154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7611.51403
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20722207
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63131120
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6264.5994
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 146
Rwork0.319 2335
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)
12.1662-0.7921-0.35954.3935-1.03523.4262-0.0569-0.15750.20260.44230.1399-0.0918-0.5074-0.046-0.0830.05580.00710.025-0.1010.0039-0.077637.83422.53849.9362
21.08840.0023-0.36921.16980.24731.39570.02720.1540.02230.04840.0573-0.043-0.0185-0.0732-0.0845-0.0516-0.0204-0.0005-0.03580.0247-0.065740.0831-20.3782-0.8686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B33 - 124
2X-RAY DIFFRACTION2B125 - 305

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