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- PDB-5lvn: Human PDK1 Kinase Domain in Complex with Adenosine Bound to the A... -

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Basic information

Entry
Database: PDB / ID: 5lvn
TitleHuman PDK1 Kinase Domain in Complex with Adenosine 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


intracellular signaling cassette / 3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation ...intracellular signaling cassette / 3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / 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 / CD28 dependent PI3K/Akt signaling / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of blood vessel endothelial cell migration / negative regulation of endothelial cell apoptotic process / vascular endothelial cell response to laminar fluid shear stress / Estrogen-stimulated signaling through PRKCZ / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / GPVI-mediated activation cascade / phospholipase binding / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / T cell costimulation / extrinsic apoptotic signaling pathway / Integrin signaling / insulin-like growth factor receptor signaling pathway / cellular response to epidermal growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / positive regulation of protein localization to plasma membrane / cell projection / 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 / FCERI mediated NF-kB activation / epidermal growth factor receptor signaling pathway / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / insulin receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cell migration / Downstream TCR signaling / PIP3 activates AKT signaling / protein autophosphorylation / actin cytoskeleton organization / cytoplasmic vesicle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein phosphorylation / non-specific serine/threonine protein kinase / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / intracellular signal transduction / 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
ADENOSINE / DITHIANE DIOL / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.379 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 2.0Oct 16, 2019Group: Atomic model / Author supporting evidence / Data collection
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_nonpoly_scheme / reflns_shell
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Jan 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
Revision 2.2Oct 16, 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)35,8474
Polymers35,3931
Non-polymers4553
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.405, 44.320, 47.670
Angle α, β, γ (deg.)90.00, 101.44, 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-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
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, 0.01 M DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91853 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: 0.91853 Å / Relative weight: 1
ReflectionResolution: 1.379→44 Å / Num. obs: 61796 / % possible obs: 99 % / Redundancy: 3 % / Net I/σ(I): 17.6

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Processing

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

3hrc


Resolution: 1.379→43.349 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.01
RfactorNum. reflection% reflection
Rfree0.1623 3090 5 %
Rwork0.1337 --
obs0.1351 61796 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.379→43.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 28 255 2525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012452
X-RAY DIFFRACTIONf_angle_d1.1353347
X-RAY DIFFRACTIONf_dihedral_angle_d14.664920
X-RAY DIFFRACTIONf_chiral_restr0.092372
X-RAY DIFFRACTIONf_plane_restr0.009425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3787-1.40030.27491340.23982558X-RAY DIFFRACTION95
1.4003-1.42320.26191390.21292630X-RAY DIFFRACTION99
1.4232-1.44780.26041400.2022660X-RAY DIFFRACTION99
1.4478-1.47410.2751400.18372662X-RAY DIFFRACTION99
1.4741-1.50240.21921400.16712667X-RAY DIFFRACTION99
1.5024-1.53310.2041400.15122655X-RAY DIFFRACTION100
1.5331-1.56640.17661400.13872658X-RAY DIFFRACTION100
1.5664-1.60290.18031410.12682679X-RAY DIFFRACTION99
1.6029-1.6430.17621400.1222672X-RAY DIFFRACTION99
1.643-1.68740.1571400.11752656X-RAY DIFFRACTION100
1.6874-1.73710.15351400.11442648X-RAY DIFFRACTION99
1.7371-1.79310.18221410.11452687X-RAY DIFFRACTION100
1.7931-1.85720.17651410.12192680X-RAY DIFFRACTION99
1.8572-1.93160.14371410.11542674X-RAY DIFFRACTION99
1.9316-2.01950.18071420.11512693X-RAY DIFFRACTION99
2.0195-2.12590.14411400.11022663X-RAY DIFFRACTION99
2.1259-2.25910.14931410.10822683X-RAY DIFFRACTION99
2.2591-2.43360.15161410.1142672X-RAY DIFFRACTION99
2.4336-2.67840.15421400.13292679X-RAY DIFFRACTION99
2.6784-3.06590.15791420.14112688X-RAY DIFFRACTION98
3.0659-3.86230.14441420.13412689X-RAY DIFFRACTION99
3.8623-43.37040.15111450.14952753X-RAY DIFFRACTION98

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