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- PDB-5lvm: Human PDK1 Kinase Domain in Complex with Adenine Bound to the ATP... -

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Basic information

Entry
Database: PDB / ID: 5lvm
TitleHuman PDK1 Kinase Domain in Complex with Adenine Bound to the ATP-Binding Site
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE / protein kinase / allosteric regulation / small compounds / PIF-pocket
Function / homology
Function and homology information


Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process ...Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / phospholipase binding / CD28 dependent PI3K/Akt signaling / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / Estrogen-stimulated signaling through PRKCZ / vascular endothelial cell response to laminar fluid shear stress / negative regulation of endothelial cell apoptotic process / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / activation of protein kinase B activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / GPVI-mediated activation cascade / extrinsic apoptotic signaling pathway / T cell costimulation / Integrin signaling / peptidyl-threonine phosphorylation / cellular response to epidermal growth factor stimulus / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / cell projection / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transforming growth factor beta receptor signaling pathway / calcium-mediated signaling / CLEC7A (Dectin-1) signaling / epidermal growth factor receptor signaling pathway / FCERI mediated NF-kB activation / cellular response to insulin stimulus / positive regulation of angiogenesis / G beta:gamma signalling through PI3Kgamma / Regulation of TP53 Degradation / insulin receptor signaling pathway / Downstream TCR signaling / cell migration / PIP3 activates AKT signaling / actin cytoskeleton organization / protein autophosphorylation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cytoplasmic vesicle / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / postsynaptic density / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PDK1-type, PH domain / PH domain / PDPK1 family / : / PH-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site ...PDK1-type, PH domain / PH domain / PDPK1 family / : / PH-like domain superfamily / 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
ADENINE / DITHIANE DIOL / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsSchulze, J.O. / Saladino, G. / Busschots, K. / Neimanis, S. / Suess, E. / Odadzic, D. / Zeuzem, S. / Hindie, V. / Herbrand, A.K. / Lisa, M.N. ...Schulze, J.O. / Saladino, G. / Busschots, K. / Neimanis, S. / Suess, E. / Odadzic, D. / Zeuzem, S. / Hindie, V. / Herbrand, A.K. / Lisa, M.N. / Alzari, P.M. / Gervasio, F.L. / Biondi, R.M.
Funding support Germany, 3items
OrganizationGrant numberCountry
BMBF GO-Bio0315102 Germany
German Research FoundationBI 1044/2-3 Germany
German Research FoundationBI 1044/12-1 Germany
CitationJournal: Cell Chem Biol / Year: 2016
Title: Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase.
Authors: Schulze, J.O. / Saladino, G. / Busschots, K. / Neimanis, S. / Su, E. / Odadzic, D. / Zeuzem, S. / Hindie, V. / Herbrand, A.K. / Lisa, M.N. / Alzari, P.M. / Gervasio, F.L. / Biondi, R.M.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Oct 16, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / reflns_shell / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6803
Polymers35,3931
Non-polymers2872
Water5,441302
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint2 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.020, 44.440, 47.780
Angle α, β, γ (deg.)90.00, 102.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3-phosphoinositide-dependent protein kinase 1 / hPDK1


Mass: 35392.566 Da / Num. of mol.: 1 / Mutation: Y288G, Q292A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDPK1, PDK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O15530, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
Details: Attention: "A" was not accepted as sample sequence. This is just adenine, not an RNA molecule.
Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, 10 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.26→44 Å / Num. obs: 82126 / % possible obs: 99.6 % / Redundancy: 6.6 % / Net I/σ(I): 17.8

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Processing

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

3hrc


Resolution: 1.26→43.641 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.89
RfactorNum. reflection% reflection
Rfree0.1549 4107 5 %
Rwork0.1335 --
obs0.1346 82121 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.26→43.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 10 8 302 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182475
X-RAY DIFFRACTIONf_angle_d1.5393380
X-RAY DIFFRACTIONf_dihedral_angle_d18.301947
X-RAY DIFFRACTIONf_chiral_restr0.114374
X-RAY DIFFRACTIONf_plane_restr0.012432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2599-1.27470.26871400.24552656X-RAY DIFFRACTION100
1.2747-1.29030.25871420.22372705X-RAY DIFFRACTION100
1.2903-1.30660.22731420.21232681X-RAY DIFFRACTION100
1.3066-1.32380.22151400.1932662X-RAY DIFFRACTION100
1.3238-1.34190.1921390.18082652X-RAY DIFFRACTION100
1.3419-1.36110.21461430.16582712X-RAY DIFFRACTION100
1.3611-1.38140.17451390.15752648X-RAY DIFFRACTION100
1.3814-1.4030.18651420.15492700X-RAY DIFFRACTION100
1.403-1.4260.20341410.15132666X-RAY DIFFRACTION100
1.426-1.45060.21561410.14212685X-RAY DIFFRACTION100
1.4506-1.4770.18831400.14052662X-RAY DIFFRACTION100
1.477-1.50540.16671410.11882677X-RAY DIFFRACTION100
1.5054-1.53610.15541420.11042689X-RAY DIFFRACTION100
1.5361-1.56950.14681400.10892659X-RAY DIFFRACTION100
1.5695-1.6060.14461420.10782712X-RAY DIFFRACTION100
1.606-1.64620.14191440.10482735X-RAY DIFFRACTION100
1.6462-1.69070.14111380.1062621X-RAY DIFFRACTION100
1.6907-1.74050.14271400.10822664X-RAY DIFFRACTION100
1.7405-1.79660.14131440.11262724X-RAY DIFFRACTION100
1.7966-1.86090.14211410.11792689X-RAY DIFFRACTION100
1.8609-1.93540.14241420.12062693X-RAY DIFFRACTION100
1.9354-2.02340.14671410.11812679X-RAY DIFFRACTION100
2.0234-2.13010.14591410.1132678X-RAY DIFFRACTION100
2.1301-2.26360.12491430.11412720X-RAY DIFFRACTION100
2.2636-2.43830.1321420.12392698X-RAY DIFFRACTION100
2.4383-2.68370.16481420.13912698X-RAY DIFFRACTION100
2.6837-3.07190.18341430.14662718X-RAY DIFFRACTION100
3.0719-3.86990.14711440.13872737X-RAY DIFFRACTION100
3.8699-43.66720.14631480.14322794X-RAY DIFFRACTION99

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