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- PDB-5n50: Crystal structure of human Pim-1 kinase in complex with a consens... -

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Basic information

Entry
Database: PDB / ID: 5n50
TitleCrystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 2-(4-chlorophenyl)sulfanylacetohydrazide
Components
  • Pimtide
  • Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / Serine Threonine Kinase / proto-oncogene / Fragment / PIM-1 / Consensus peptide
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-(4-chlorophenyl)sulfanylethanehydrazide / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSiefker, C. / Heine, A. / Klebe, G.
CitationJournal: to be published
Title: A crystallographic fragment study with human Pim-1 kinase
Authors: Siefker, C. / Heine, A. / Hardes, K. / Steinmetzer, A. / Klebe, G.
History
DepositionFeb 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Pimtide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4423
Polymers37,2252
Non-polymers2171
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint3 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.315, 98.315, 80.504
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: 35632.602 Da / Num. of mol.: 1 / Mutation: R250G
Source method: isolated from a genetically manipulated source
Details: Isofrom 2 of PIM-1 kinase / Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pLIC-SGC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Protein/peptide Pimtide


Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PIM-1 consensus peptide / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-8MN / 2-(4-chlorophenyl)sulfanylethanehydrazide


Mass: 216.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9ClN2OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.15 Å3/Da / Density % sol: 61 % / Description: hexagonal rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: HEPES CaCl2 Glycerol DTT BIS-TRIS-propane PEG3350 Ethylene-glycol DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 27, 2016 / Details: Silicon
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 33834 / % possible obs: 99.9 % / Redundancy: 7.99 % / CC1/2: 0.99 / Rrim(I) all: 0.086 / Net I/σ(I): 15.01
Reflection shellResolution: 1.92→2.04 Å / Redundancy: 8.07 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 5425 / CC1/2: 0.91 / Rrim(I) all: 0.544 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WE8

3we8


Resolution: 1.92→41.954 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 1692 5 %
Rwork0.1584 --
obs0.1595 33828 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→41.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 13 186 2443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072358
X-RAY DIFFRACTIONf_angle_d0.753202
X-RAY DIFFRACTIONf_dihedral_angle_d20.2311395
X-RAY DIFFRACTIONf_chiral_restr0.053338
X-RAY DIFFRACTIONf_plane_restr0.005427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9195-1.9760.22131390.21052649X-RAY DIFFRACTION100
1.976-2.03980.23751410.17092666X-RAY DIFFRACTION100
2.0398-2.11270.19771400.16162674X-RAY DIFFRACTION100
2.1127-2.19730.1911410.16242664X-RAY DIFFRACTION100
2.1973-2.29730.19631400.15232666X-RAY DIFFRACTION100
2.2973-2.41840.19451410.1532675X-RAY DIFFRACTION100
2.4184-2.56990.18881410.15682677X-RAY DIFFRACTION100
2.5699-2.76830.2111410.1692679X-RAY DIFFRACTION100
2.7683-3.04680.20461400.16772671X-RAY DIFFRACTION100
3.0468-3.48750.17831420.16482696X-RAY DIFFRACTION100
3.4875-4.39310.16781420.14232691X-RAY DIFFRACTION100
4.3931-41.96430.15181440.15752728X-RAY DIFFRACTION100
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)
10.7699-0.628-0.38030.63770.34871.77230.0683-0.01210.5174-0.05380.1531-0.1321-0.72840.34910.19050.43310.0210.06430.26180.01680.3887-87.136789.9909-9.9447
21.10860.1872-0.14571.2682-0.14911.9960.1015-0.0473-0.0267-0.034-0.01620.0107-0.06670.035500.20570.0283-0.00360.2003-0.02330.2002-88.926568.0616-3.922
30.5658-0.1484-0.05710.1088-0.04290.059-0.1572-0.526-0.14110.10980.1038-0.2223-0.05870.1461-0.01020.4397-0.0487-0.01160.3998-0.10340.3598-84.240473.79849.6456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 305 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 10 )

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