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- PDB-5n4u: Crystal structure of human Pim-1 kinase in complex with a consens... -

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Basic information

Entry
Database: PDB / ID: 5n4u
TitleCrystal structure of human Pim-1 kinase in complex with a consensuspeptide and fragment like molekule 5-(2-amino-1,3-thiazol-4-yl)-1,3-dihydrobenzimidazol-2-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 / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / 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
Chem-8MZ / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 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)37,4583
Polymers37,2252
Non-polymers2321
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint2 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.911, 97.911, 80.573
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-8MZ / 5-(2-azanyl-1,3-thiazol-4-yl)-1,3-dihydrobenzimidazol-2-one


Mass: 232.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N4OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.12 Å3/Da / Density % sol: 61 % / Description: hexagonal rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: HEPES NaCl Glycerol DTT BIS-TRIS-propane PEG3350 Ethylene-glycol DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2016 / Details: Silicon
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 22315 / % possible obs: 99.9 % / Redundancy: 6.91 % / CC1/2: 0.99 / Rrim(I) all: 0.063 / Net I/σ(I): 20.97
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 7.01 % / Mean I/σ(I) obs: 3.86 / Num. unique obs: 3570 / CC1/2: 0.91 / Rrim(I) all: 0.541 / % possible all: 99.5

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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: 2.202→42.397 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 1116 5 %
Rwork0.1636 --
obs0.1653 22314 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→42.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 16 91 2336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142318
X-RAY DIFFRACTIONf_angle_d1.0663148
X-RAY DIFFRACTIONf_dihedral_angle_d22.7491368
X-RAY DIFFRACTIONf_chiral_restr0.071335
X-RAY DIFFRACTIONf_plane_restr0.007428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2017-2.30190.24481380.19582627X-RAY DIFFRACTION99
2.3019-2.42320.23441390.17422631X-RAY DIFFRACTION100
2.4232-2.5750.21381390.17082648X-RAY DIFFRACTION100
2.575-2.77380.23861390.17642640X-RAY DIFFRACTION100
2.7738-3.05290.21771390.17342635X-RAY DIFFRACTION100
3.0529-3.49440.20351400.17322660X-RAY DIFFRACTION100
3.4944-4.40190.17991390.15012649X-RAY DIFFRACTION100
4.4019-42.40450.17441430.15532708X-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)
10.1625-0.15590.05070.15-0.0530.0255-0.18470.46750.1899-0.0841-0.15240.1825-0.2739-0.71530.00030.9716-0.07570.02360.59270.00940.7716138.33417.41132.599
20.2078-0.02340.0620.62210.16280.8302-0.3009-0.02560.07660.59750.23420.1469-0.3928-0.146-0.00310.57-0.00880.05380.4638-0.01410.4651133.07441.43219.8108
30.3066-0.42320.48170.8301-0.62130.8014-0.0071-0.07580.23570.07090.1946-0.3186-0.50960.22960.02720.4735-0.04420.05140.3706-0.00610.3862141.1735-3.35763.1826
41.3495-0.0554-0.36621.1289-0.03452.28540.09550.0573-0.0719-0.00150.0217-0.00980.1496-0.060600.3253-0.0302-0.020.310.0350.328137.1613-21.0107-1.0167
50.0145-0.00350.00860.0251-0.0130.0199-0.03820.29970.21410.1630.22350.1803-0.3237-0.40070.11390.58570.10390.05410.39610.180.4603133.1844-9.853-11.5468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 140 )
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 305 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 9 )

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