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- PDB-8r1k: Pim1 in complex with 6-bromobenzo[d]oxazol-2-amine and Pimtide -

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Basic information

Entry
Database: PDB / ID: 8r1k
TitlePim1 in complex with 6-bromobenzo[d]oxazol-2-amine 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 / 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 / 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: 1.95 Å
AuthorsHochban, P.M.M. / Heine, A. / Diederich, W.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Pim1 in complex with 6-bromobenzo[d]oxazol-2-amine and Pimtide
Authors: Hochban, P.M.M. / Hubach, D. / Heine, A. / Diederich, W.E.
History
DepositionNov 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)37,6615
Polymers37,2632
Non-polymers3973
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint3 kcal/mol
Surface area12590 Å2
Unit cell
Length a, b, c (Å)97.619, 97.619, 80.248
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

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-XHI / 6-bromanyl-1,3-benzoxazol-2-amine


Mass: 213.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5BrN2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 60.4 %
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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→48.81 Å / Num. obs: 31728 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 49.36 Å2 / CC1/2: 0.99 / Net I/σ(I): 24
Reflection shellResolution: 1.95→1.96 Å / Num. unique obs: 5104 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.20.1_4487refinement
XDS3.1.9data reduction
XDS3.1.9data scaling
PHASERphasing
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.81 Å / SU ML: 0.2069 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.4231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1921 1587 5 %
Rwork0.1764 30126 -
obs0.1772 31713 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.58 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 23 88 2309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072280
X-RAY DIFFRACTIONf_angle_d0.75863098
X-RAY DIFFRACTIONf_chiral_restr0.0515333
X-RAY DIFFRACTIONf_plane_restr0.0086402
X-RAY DIFFRACTIONf_dihedral_angle_d12.8705819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.2751440.2362724X-RAY DIFFRACTION99.9
2.01-2.080.20931420.2012711X-RAY DIFFRACTION99.89
2.08-2.170.23211450.20222739X-RAY DIFFRACTION99.9
2.17-2.270.21521430.18642728X-RAY DIFFRACTION99.9
2.27-2.390.20681440.1742721X-RAY DIFFRACTION99.86
2.39-2.540.19811430.18682722X-RAY DIFFRACTION100
2.54-2.730.23821450.19912752X-RAY DIFFRACTION100
2.73-3.010.21121440.18532737X-RAY DIFFRACTION100
3.01-3.440.1981440.18732735X-RAY DIFFRACTION100
3.44-4.330.20281450.16122765X-RAY DIFFRACTION100
4.34-48.810.15791480.1692792X-RAY DIFFRACTION99.73
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)
11.84194932867-0.0514555871447-0.2472620595591.82732201875-0.469373639822.515539583860.0504754435804-0.0604954784270.04222735385190.09344940245450.0532130838844-0.0593152788180.1187977233030.179333828489-1.43914883403E-50.388860331217-0.004358093056720.01224029421740.457182310296-0.03087001950830.411710842526-50.1572968957-128.681063095-0.00850795523926
20.9581083648220.7711701187660.1740854146670.6274296748510.1459393011620.03385102283470.86939100799-0.8383496616260.5342825781910.607671943853-0.659944301914-0.16857236649-0.2734920382830.4494526026070.01830246288760.6539724163280.05548125053440.1671805248320.595289886556-0.08448763949760.625941174027-57.4144744038-118.92404451710.2857605931
30.0702689689272-0.0833151683889-0.01450421877590.2265832830910.08347110209180.09335232437550.360577281413-0.3245778079960.3152740834830.640150307522-0.3617284948030.246583397366-0.480629276010.6594498173980.0003610101078010.6516350839380.0453334084955-0.02414094155961.115129853180.0125164610210.907895022156-76.30339095-115.649450445-4.60634493738
40.561289987997-0.5247125135110.3042749538860.771518787408-0.2631461351770.8953273138420.496000667626-0.05209949077420.430070861339-0.356122771151-0.4806912826570.132479379287-0.448632602396-0.2157208463620.0001129599076370.4989376133930.01073887794520.0553312862220.6191135892750.01130838849150.566881807752-67.8320116583-114.432511522-10.6816540015
50.470616854264-0.506126430939-0.01694790258421.057898200060.8287517736910.9636697412550.0590553510325-0.194428348152-0.0622216462377-0.2149904802130.07165552378360.2857387829330.109368549246-0.703157499638-0.0001954775848930.4460215674790.01186852235750.03887888706240.6368368190250.0246580595420.517497167041-67.4992355767-123.167707434-3.83725770346
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 'B' and (resid 3 through 10 )BC3 - 101 - 8
33chain 'A' and (resid 33 through 49 )AA33 - 491 - 17
44chain 'A' and (resid 50 through 96 )AA50 - 9618 - 64
55chain 'A' and (resid 97 through 140 )AA97 - 14065 - 108

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