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

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Basic information

Entry
Database: PDB / ID: 5mzl
TitleCrystal structure of human Pim-1 kinase in complex with a consensuspeptide and fragment like molekule N-quinolin-5-ylpyridine-3-carboxamide
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
~{N}-quinolin-5-ylpyridine-3-carboxamide / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 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 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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)37,5674
Polymers37,2252
Non-polymers3412
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint4 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.942, 97.942, 80.162
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: Isoform 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 fragment / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-8ET / ~{N}-quinolin-5-ylpyridine-3-carboxamide


Mass: 249.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11N3O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.1 Å3/Da / Density % sol: 60.29 % / 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 3, 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: 1.955→50 Å / Num. obs: 31579 / % possible obs: 99.6 % / Redundancy: 6.19 % / CC1/2: 0.99 / Rrim(I) all: 0.046 / Net I/σ(I): 24.44
Reflection shellResolution: 1.955→2.07 Å / Redundancy: 6.07 % / Mean I/σ(I) obs: 5.01 / Num. unique obs: 5033 / CC1/2: 0.9 / % possible all: 98.5

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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: 1.955→42.41 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.48
RfactorNum. reflection% reflection
Rfree0.1834 1578 5 %
Rwork0.157 --
obs0.1584 31570 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.955→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 25 120 2364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032316
X-RAY DIFFRACTIONf_angle_d0.5913142
X-RAY DIFFRACTIONf_dihedral_angle_d20.4041381
X-RAY DIFFRACTIONf_chiral_restr0.046335
X-RAY DIFFRACTIONf_plane_restr0.004426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9545-2.01760.2681390.22892649X-RAY DIFFRACTION97
2.0176-2.08970.22811430.18532713X-RAY DIFFRACTION100
2.0897-2.17340.19481430.17582716X-RAY DIFFRACTION100
2.1734-2.27230.181430.16192726X-RAY DIFFRACTION100
2.2723-2.39210.17911440.15742724X-RAY DIFFRACTION100
2.3921-2.5420.17411440.15772730X-RAY DIFFRACTION100
2.542-2.73820.19731430.16862730X-RAY DIFFRACTION100
2.7382-3.01370.18261450.16432747X-RAY DIFFRACTION100
3.0137-3.44960.18231430.16432724X-RAY DIFFRACTION100
3.4496-4.34540.18521450.14212752X-RAY DIFFRACTION100
4.3454-42.42010.17141460.15042781X-RAY DIFFRACTION99
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)
10.6181-0.0235-0.27290.00140.01650.2161-0.4032-0.7961-0.5065-0.0310.0158-0.21840.4109-0.1137-0.02330.74450.12210.01660.48310.03520.6795189.010774.5481-8.4141
20.27320.1824-0.16510.1882-0.02170.21780.05270.1441-0.1054-0.5582-0.01280.24680.6967-0.1017-00.58430.0237-0.06870.45860.01250.4502181.739782.5659-13.0798
30.29410.1027-0.39020.7515-0.50890.79890.01540.1034-0.1318-0.04810.1239-0.13680.38110.2746-00.49380.0364-0.02580.4136-0.01450.3763189.632688.4663-7.3822
41.1492-0.0698-0.01841.3267-0.00332.07730.0682-0.00550.09280.0475-0.06130.0886-0.04240.0389-00.30530.01850.02720.31730.00660.3378186.0325105.8087-2.404
50.19-0.03290.05290.0086-0.02170.0822-0.2325-0.63880.15370.02350.1865-0.0737-0.1802-0.3818-0.00610.6234-0.07210.03530.45660.05190.4135182.469696.0619.9947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 140 )
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 305 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 9 )

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