[English] 日本語
Yorodumi
- PDB-8dqt: Human PDK1 kinase domain in complex with Valsartan -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dqt
TitleHuman PDK1 kinase domain in complex with Valsartan
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE / AGC KINASE / PHOSPHORYLATION / PDK1 / PIF-POCKET / ALPHA-C HELIX / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / KINASE TRANSFERASE
Function / homology
Function and homology information


intracellular signaling cassette / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / 3-phosphoinositide-dependent protein kinase activity / RSK activation / regulation of canonical NF-kappaB signal transduction / hyperosmotic response / positive regulation of vascular endothelial cell proliferation ...intracellular signaling cassette / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / 3-phosphoinositide-dependent protein kinase activity / RSK activation / regulation of canonical NF-kappaB signal transduction / hyperosmotic response / 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 / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of endothelial cell apoptotic process / Estrogen-stimulated signaling through PRKCZ / vascular endothelial cell response to laminar fluid shear stress / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / phospholipase binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / GPVI-mediated activation cascade / RHO GTPases activate PKNs / 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 / 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 / FCERI mediated NF-kB activation / epidermal growth factor receptor signaling pathway / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / Downstream TCR signaling / G beta:gamma signalling through PI3Kgamma / insulin receptor signaling pathway / cell migration / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / 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 / 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 ...PDK1-type, PH domain / PH domain / PDPK1 family / : / PH-like domain superfamily / 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
Chem-U35 / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsGross, L.Z.F. / Klinke, S. / Biondi, R.M.
Funding support Argentina, 1items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2016-3525 Argentina
CitationJournal: Sci.Signal. / Year: 2023
Title: Modulation of the substrate specificity of the kinase PDK1 by distinct conformations of the full-length protein.
Authors: Sacerdoti, M. / Gross, L.Z.F. / Riley, A.M. / Zehnder, K. / Ghode, A. / Klinke, S. / Anand, G.S. / Paris, K. / Winkel, A. / Herbrand, A.K. / Godage, H.Y. / Cozier, G.E. / Suss, E. / Schulze, ...Authors: Sacerdoti, M. / Gross, L.Z.F. / Riley, A.M. / Zehnder, K. / Ghode, A. / Klinke, S. / Anand, G.S. / Paris, K. / Winkel, A. / Herbrand, A.K. / Godage, H.Y. / Cozier, G.E. / Suss, E. / Schulze, J.O. / Pastor-Flores, D. / Bollini, M. / Cappellari, M.V. / Svergun, D. / Grawert, M.A. / Aramendia, P.F. / Leroux, A.E. / Potter, B.V.L. / Camacho, C.J. / Biondi, R.M.
History
DepositionJul 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,7915
Polymers35,3931
Non-polymers1,3994
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.510, 44.590, 48.210
Angle α, β, γ (deg.)90.000, 101.320, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
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-U35 / (2~{S})-3-methyl-2-[pentanoyl-[[4-[2-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]amino]butanoic acid / (2~{S})-3-methyl-2-[pentanoyl-[[4-[2-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]amino]butanoic acid / Diovan / Tareg / Provas / Exforge / N-(p-(o-1H-Tetrazol-5-ylphenyl)benzyl)-N-valeryl-L-valine


Mass: 435.519 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H29N5O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.61 % / Description: Bipyramids
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.2M sodium citrate, 0.1M Hepes pH 7.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2019
Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.31→47.27 Å / Num. obs: 73419 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.37 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 15.9
Reflection shellResolution: 1.31→1.39 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 11539 / CC1/2: 0.744 / Rrim(I) all: 1.306 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HRC

3hrc


Resolution: 1.31→36.51 Å / SU ML: 0.1982 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4433
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 3664 5 %
Rwork0.1991 69636 -
obs0.2004 73300 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.98 Å2
Refinement stepCycle: LAST / Resolution: 1.31→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 0 133 2590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952521
X-RAY DIFFRACTIONf_angle_d1.10873403
X-RAY DIFFRACTIONf_chiral_restr0.0966355
X-RAY DIFFRACTIONf_plane_restr0.0084431
X-RAY DIFFRACTIONf_dihedral_angle_d20.3682343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.330.38861220.37822320X-RAY DIFFRACTION88.38
1.33-1.350.36071420.35762705X-RAY DIFFRACTION99.44
1.35-1.370.38151400.34712645X-RAY DIFFRACTION99.46
1.37-1.390.36621420.33692694X-RAY DIFFRACTION99.61
1.39-1.410.35361410.3282673X-RAY DIFFRACTION99.61
1.41-1.430.3781410.3172690X-RAY DIFFRACTION99.61
1.43-1.460.36151380.32142653X-RAY DIFFRACTION99.54
1.46-1.490.3491410.33492661X-RAY DIFFRACTION99.61
1.49-1.510.35161430.32342704X-RAY DIFFRACTION99.55
1.51-1.540.32151390.27272650X-RAY DIFFRACTION99.75
1.54-1.580.31411410.25922667X-RAY DIFFRACTION99.93
1.58-1.610.32251420.23962710X-RAY DIFFRACTION99.96
1.61-1.660.24441410.22262678X-RAY DIFFRACTION99.89
1.66-1.70.22861420.20482696X-RAY DIFFRACTION99.89
1.7-1.750.24231400.19742653X-RAY DIFFRACTION99.75
1.75-1.810.19751410.19582697X-RAY DIFFRACTION99.68
1.81-1.870.2231420.19492691X-RAY DIFFRACTION99.58
1.87-1.950.18641420.17962698X-RAY DIFFRACTION99.79
1.95-2.030.19121410.17952689X-RAY DIFFRACTION99.37
2.03-2.140.22781410.18192681X-RAY DIFFRACTION99.68
2.14-2.280.21461420.18262701X-RAY DIFFRACTION99.93
2.28-2.450.20781430.19592709X-RAY DIFFRACTION99.79
2.45-2.70.21921420.19612706X-RAY DIFFRACTION99.75
2.7-3.090.20871440.19612729X-RAY DIFFRACTION99.58
3.09-3.890.20211440.17662728X-RAY DIFFRACTION99.83
3.89-36.510.19681470.17022808X-RAY DIFFRACTION99.53

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more