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- PDB-8r18: Pim1 in complex with (E)-4-(4-hydroxystyryl)benzoic acid and Pimtide -

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Basic information

Entry
Database: PDB / ID: 8r18
TitlePim1 in complex with (E)-4-(4-hydroxystyryl)benzoic acid and Pimtide
Components
  • Pimtide
  • Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / SERINE KINASE / KINASE / COMPLEX / PIM1 / PIM / PIM-1 / INHIBITOR / TUMORIGENISIS / CANCER / PIMTIDE / PROTO ONCOGEN / ATP / PHOSPHORYLATION / APOPTOSIS / CELL CYCLE
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / 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 / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / 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 / 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 / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / 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
Similarity search - Domain/homology
: / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHochban, P.M.M. / Heine, A. / Diederich, W.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch Pharm / Year: 2024
Title: What doesn't fit is made to fit: Pim-1 kinase adapts to the configuration of stilbene-based inhibitors.
Authors: Hochban, P.M.M. / Heyder, L. / Heine, A. / Diederich, W.E.
History
DepositionNov 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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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
C: Pimtide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6585
Polymers37,2632
Non-polymers3943
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.507, 96.507, 80.201
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Serine/threonine-protein kinase pim-1


Mass: 35670.477 Da / Num. of mol.: 1 / Mutation: R250G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli BL21(DE3) (bacteria)
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)

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Non-polymers , 4 types, 184 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-XGK / (E)-4-(4-hydroxystyryl)benzoic acid / 4-[(E)-2-(4-hydroxyphenyl)ethenyl]benzoic acid


Mass: 240.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM bis-tris-propane (pH 7.0), 10% ethylene glycol, 0.3% DMSO, 20% PEG3350, 200 mM Mg(OAc)2
PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2020
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.89→48.25 Å / Num. obs: 33686 / % possible obs: 98.8 % / Redundancy: 10.3 % / Biso Wilson estimate: 31.58 Å2 / CC1/2: 0.99 / Net I/σ(I): 20
Reflection shellResolution: 1.89→1.9 Å / Mean I/σ(I) obs: 3.9 / Num. unique obs: 5369 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
XDS1.02data reduction
XDS1.02data scaling
PHASERphasing
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→48.25 Å / SU ML: 0.1719 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.6426
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1856 1685 5 %
Rwork0.1596 31987 -
obs0.1609 33672 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.14 Å2
Refinement stepCycle: LAST / Resolution: 1.89→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 28 181 2455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722391
X-RAY DIFFRACTIONf_angle_d0.79343248
X-RAY DIFFRACTIONf_chiral_restr0.0539344
X-RAY DIFFRACTIONf_plane_restr0.0083440
X-RAY DIFFRACTIONf_dihedral_angle_d12.1164879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.2421380.20292624X-RAY DIFFRACTION97.98
1.94-2.010.18331390.1872623X-RAY DIFFRACTION97.84
2.01-2.080.21380.16072630X-RAY DIFFRACTION97.6
2.08-2.160.16711400.1572660X-RAY DIFFRACTION98.73
2.16-2.260.18111400.15332653X-RAY DIFFRACTION99.08
2.26-2.380.17891400.15232661X-RAY DIFFRACTION98.98
2.38-2.530.21321410.16722688X-RAY DIFFRACTION99.3
2.53-2.720.2051400.17822649X-RAY DIFFRACTION98.48
2.72-30.18891410.16992686X-RAY DIFFRACTION99.51
3-3.430.1991420.16842694X-RAY DIFFRACTION99.68
3.43-4.320.17711410.14252686X-RAY DIFFRACTION98.92
4.32-48.250.16961450.15412733X-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)
10.8920692983120.1433551719230.6214916677991.708962302830.1789116046472.331053232420.100132733027-0.080074744117-0.02653551895350.0586116640149-0.02632144300080.0793128827256-0.0948413909748-0.04152394692589.18035587981E-50.2001513388950.02366691731640.0152246262850.2092227485580.01065078959290.206489883183.125117128104.1797377052.99599952817
20.06380021736090.0244966483254-0.05830420813310.0397962680648-0.0400052472260.06219528142270.0413928975822-0.443779045733-0.01209687926780.06331921592130.1252628648040.1632699952850.0407820631598-0.4241818489760.0003000024726020.548130928812-0.108013041521-0.003234008360320.4074461546210.05914614809220.368851949461179.45167847994.366197247115.661897943
31.204734384330.0278216229018-0.3089768761430.00115082847233-0.008264122817910.0798337663484-0.174430618353-0.606255639029-0.457007609042-0.00788689299328-0.1452219319510.23449489192-0.3512636070160.0856976019731-0.06227436700690.7269390469720.02935536609450.1042608343360.37970883890.04124407620990.71675810565185.68715571674.3540264157-1.00422779455
40.4070609624910.067965826144-0.1314666876010.769535984759-0.260431312860.863976408467-0.086761339673-0.0611061172382-0.131290160531-0.6492049186360.04869080917290.1020881279210.460687814682-0.200684794215-0.02981628644830.447735196521-0.000233564885212-0.0589222595070.2727774543740.01472633659530.3863187321179.43721178481.5133098969-8.1344044564
50.346263159240.297038184878-0.5197019110850.717674667659-0.5367268764990.789255180351-0.000239511373864-0.0753077691834-0.2605668944090.1491189572190.109441795942-0.1368379326340.5737082724010.1239070786970.007072928268680.3741294128330.0462096709544-0.04360027514620.246173897790.002910099760470.33304601567187.15694268186.6589726787-1.0579435557
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 141 through 305 )AA141 - 305109 - 273
22chain 'C' and (resid 1 through 10 )CC1 - 101 - 10
33chain 'A' and (resid 33 through 50 )AA33 - 501 - 18
44chain 'A' and (resid 51 through 95 )AA51 - 9519 - 63
55chain 'A' and (resid 96 through 140 )AA96 - 14064 - 108

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