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- PDB-5n4r: Crystal structure of human Pim-1 kinase in complex with a consens... -

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Basic information

Entry
Database: PDB / ID: 5n4r
TitleCrystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 2-(azepan-1-yl)-1-(1H-indol-3-yl)propan-1-one
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 / 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 cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response ...positive regulation of cardioblast proliferation / 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 cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / positive regulation of TORC1 signaling / 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 / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / nucleolus / 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 ...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
2-(azepan-1-yl)-1-(1~{H}-indol-3-yl)propan-1-one / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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
E: Pimtide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5884
Polymers37,2252
Non-polymers3622
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint2 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.121, 98.121, 80.457
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 / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-8MQ / 2-(azepan-1-yl)-1-(1~{H}-indol-3-yl)propan-1-one


Mass: 270.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N2O
#5: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 61 % / Description: hexagonal rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: HHEPES Li2SO4 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 26, 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: 2.13→50 Å / Num. obs: 24738 / % possible obs: 99.9 % / Redundancy: 6.89 % / CC1/2: 0.99 / Rrim(I) all: 0.075 / Net I/σ(I): 16.46
Reflection shellResolution: 2.13→2.26 Å / Redundancy: 7.01 % / Mean I/σ(I) obs: 3.53 / Num. unique obs: 3965 / CC1/2: 0.88 / Rrim(I) all: 0.542 / % possible all: 99.6

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Processing

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

3we8


Resolution: 2.13→49.06 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.21
RfactorNum. reflection% reflection
Rfree0.1933 1237 5 %
Rwork0.1601 --
obs0.1618 24732 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.13→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 18 132 2365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072303
X-RAY DIFFRACTIONf_angle_d0.7943128
X-RAY DIFFRACTIONf_dihedral_angle_d21.7231355
X-RAY DIFFRACTIONf_chiral_restr0.053336
X-RAY DIFFRACTIONf_plane_restr0.005419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1291-2.21430.27161360.20622593X-RAY DIFFRACTION99
2.2143-2.31510.22091370.17652604X-RAY DIFFRACTION100
2.3151-2.43720.2291370.16792598X-RAY DIFFRACTION100
2.4372-2.58990.22681370.1652613X-RAY DIFFRACTION100
2.5899-2.78980.19071370.16552584X-RAY DIFFRACTION100
2.7898-3.07050.18931370.16442611X-RAY DIFFRACTION100
3.0705-3.51470.1841380.1582617X-RAY DIFFRACTION100
3.5147-4.42770.17321380.14392619X-RAY DIFFRACTION100
4.4277-49.07350.18971400.16042656X-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)
10.4083-0.58370.10620.90480.10220.5827-0.13530.04150.30640.41090.21150.2395-0.3851-0.14390.00010.5135-0.03070.04150.3422-0.01240.452134.88062.83497.9622
20.32640.21560.34870.9714-0.46330.8457-0.0232-0.0120.3337-0.03940.1742-0.2792-0.44250.23390.0040.4028-0.02370.01220.30730.00020.3281141.1183-3.31362.6741
31.58720.1821-0.38091.3634-0.01472.55320.07310.068-0.05710.00640.0234-0.00140.1543-0.0501-00.2289-0.0364-0.02280.19220.0250.2186137.435-21.1303-0.9587
40.0515-0.01120.07580.0365-0.00070.0594-0.29360.40060.4760.29920.33410.471-0.2646-0.7154-0.00040.48780.08750.0490.43880.13540.4051133.2068-10.0474-11.6152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 305 )
4X-RAY DIFFRACTION4chain 'E' and (resid 3 through 9 )

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