[English] 日本語
Yorodumi
- PDB-1h1w: High resolution crystal structure of the human PDK1 catalytic domain -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1h1w
TitleHigh resolution crystal structure of the human PDK1 catalytic domain
Components3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1
KeywordsTRANSFERASE / PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE / PKA / AGC KINASE ACTIVATION / PIF-POCKET / PI3-KINASE SIGNALLING / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING
Function / homologyDownstream TCR signaling / Protein kinase domain profile. / Role of LAT2/NTAL/LAB on calcium mobilization / Integrin alphaIIb beta3 signaling / Protein kinase domain / Serine/threonine-protein kinase, active site / Protein kinase-like domain superfamily / PH-like domain superfamily / Protein kinase, ATP binding site / PDK1-type, PH domain ...Downstream TCR signaling / Protein kinase domain profile. / Role of LAT2/NTAL/LAB on calcium mobilization / Integrin alphaIIb beta3 signaling / Protein kinase domain / Serine/threonine-protein kinase, active site / Protein kinase-like domain superfamily / PH-like domain superfamily / Protein kinase, ATP binding site / PDK1-type, PH domain / CD28 dependent PI3K/Akt signaling / PDPK1 family / Protein kinase domain / FCERI mediated NF-kB activation / Protein kinases ATP-binding region signature. / Serine/Threonine protein kinases active-site signature. / PH domain / Activation of AKT2 / VEGFR2 mediated vascular permeability / Regulation of TP53 Degradation / Constitutive Signaling by AKT1 E17K in Cancer / RHO GTPases activate PKNs / VEGFR2 mediated cell proliferation / CLEC7A (Dectin-1) signaling / RSK activation / G beta:gamma signalling through PI3Kgamma / PIP3 activates AKT signaling / GPVI-mediated activation cascade / 3-phosphoinositide-dependent protein kinase activity / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / phospholipase activator activity / regulation of I-kappaB kinase/NF-kappaB signaling / hyperosmotic response / positive regulation of phospholipase activity / cellular response to brain-derived neurotrophic factor stimulus / focal adhesion assembly / phospholipase binding / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / positive regulation of sprouting angiogenesis / extrinsic apoptotic signaling pathway / negative regulation of endothelial cell apoptotic process / positive regulation of blood vessel endothelial cell migration / cell projection / negative regulation of protein kinase activity / calcium-mediated signaling / cellular response to epidermal growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / T cell costimulation / activation of protein kinase B activity / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of protein localization to plasma membrane / actin cytoskeleton organization / Fc-epsilon receptor signaling pathway / epidermal growth factor receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / insulin receptor binding / cellular response to insulin stimulus / positive regulation of angiogenesis / cell migration / peptidyl-threonine phosphorylation / platelet activation / cytoplasmic vesicle / T cell receptor signaling pathway / perikaryon / negative regulation of neuron apoptotic process / kinase activity / postsynaptic density / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein autophosphorylation / focal adhesion / protein serine/threonine kinase activity / protein phosphorylation / protein kinase binding / nucleoplasm / ATP binding / plasma membrane / cytosol / cytoplasm / 3-phosphoinositide-dependent protein kinase 1
Function and homology information
Specimen sourceHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2 Å resolution
AuthorsBiondi, R.M. / Komander, D. / Thomas, C.C. / Lizcano, J.M. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
CitationJournal: Embo J. / Year: 2003
Title: High Resolution Crystal Structure of the Human Pdk1 Catalytic Domain Defines the Regulatory Phosphopeptide Docking Site
Authors: Biondi, R.M. / Komander, D. / Thomas, C.C. / Lizcano, J.M. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 23, 2002 / Release: Jul 17, 2003
RevisionDateData content typeGroupProviderType
1.0Jul 17, 2003Structure modelrepositoryInitial release
1.1Sep 14, 2011Structure modelDerived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance

-
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)35,17715
Polyers33,4521
Non-polymers1,72414
Water3,603200
1
A: 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1
hetero molecules

A: 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,35330
Polyers66,9052
Non-polymers3,44828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area (Å2)9510
ΔGint (kcal/M)-173.6
Surface area (Å2)24620
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)123.013, 123.013, 47.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP 32 2 1

-
Components

#1: Protein/peptide 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 / HPDK1


Mass: 33452.469 Da / Num. of mol.: 1 / Details: ACTIVATION LOOP PHOSPHORYLATION (SER241) / Fragment: KINASE CATALYTIC DOMAIN, RESIDUES 71-359 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21
References: UniProt: O15530, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Formula: C3H8O3 / Glycerol
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Formula: SO4 / Sulfate
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 / Density percent sol: 55.9 %
Crystal growpH: 8.5
Details: 0.1 M TRIS/HCL PH 8.5, 2.0 M AMMONIUM SULPHATE, 16.6 MM ATP
Crystal grow
*PLUS
Temp: 20 ℃ / pH: 8.5 / Method: vapor diffusion, sitting drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
1100 mMEDTA1drop
20.1 MTris-HCl1droppH8.5
32.0 Mammonium sulfate1drop
416.6 mMATP1drop
50.1 MTris-HCl1reservoirpH8.5
62.0 Mammonium sulfate1reservoir
716.6 mMATP1reservoir

-
Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID14-1 / Synchrotron site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Details: MIRRORS / Detector: CCD / Collection date: Mar 4, 2002
RadiationMonochromator: THIN DIAMOND CRYSTAL / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 12.6 Å2 / D resolution high: 2 Å / D resolution low: 25 Å / Number obs: 27643 / Rmerge I obs: 0.091 / NetI over sigmaI: 7.3 / Redundancy: 2.8 % / Percent possible obs: 98
Reflection shellRmerge I obs: 0.454 / Highest resolution: 2 Å / Lowest resolution: 2.07 Å / MeanI over sigI obs: 2 / Redundancy: 2.5 % / Percent possible all: 93.5
Reflection
*PLUS
D resolution high: 2 Å / D resolution low: 25 Å / Number measured all: 77315 / Rmerge I obs: 0.091 / Redundancy: 2.8 %
Reflection shell
*PLUS
Highest resolution: 2 Å / Percent possible obs: 93.5 / Rmerge I obs: 0.454 / Redundancy: 2.5 % / MeanI over sigI obs: 2

+
Processing

Software
NameVersionClassification
CNS1.0refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YDB
R Free selection details: RANDOM / Data cutoff high absF: 2010867.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 51.6939 / Solvent model param ksol: 0.380238
Displacement parametersB iso mean: 27.9 Å2 / Aniso B11: 2.76 Å2 / Aniso B12: 0.39 Å2 / Aniso B13: 0 Å2 / Aniso B22: 2.76 Å2 / Aniso B23: 0 Å2 / Aniso B33: -5.52 Å2
Least-squares processR factor R free: 0.223 / R factor R free error: 0.009 / R factor R work: 0.196 / R factor obs: 0.196 / Highest resolution: 2 Å / Lowest resolution: 24.44 Å / Number reflection R free: 579 / Number reflection obs: 27642 / Percent reflection R free: 2.1 / Percent reflection obs: 97.9
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.26 Å / Luzzati sigma a obs: 0.24 Å
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 24.44 Å
Number of atoms included #LASTProtein: 2295 / Nucleic acid: 0 / Ligand: 104 / Solvent: 200 / Total: 2599
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.501.50
X-RAY DIFFRACTIONc_mcangle_it2.352.00
X-RAY DIFFRACTIONc_scbond_it2.232.00
X-RAY DIFFRACTIONc_scangle_it3.302.50
Refine LS shellHighest resolution: 2 Å / R factor R free: 0.276 / R factor R free error: 0.03 / R factor R work: 0.263 / Lowest resolution: 2.13 Å / Number reflection R free: 84 / Number reflection R work: 4355 / Total number of bins used: 6 / Percent reflection R free: 1.9 / Percent reflection obs: 95.4
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROT.PARAMPROT.TOP
X-RAY DIFFRACTION2ATP.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMGLYC.TOP
X-RAY DIFFRACTION4ION.PARAMATP.TOP
X-RAY DIFFRACTION5GLYC.PARAMION.TOP
Least-squares process
*PLUS
R factor R free: 0.222 / R factor R work: 0.195 / Highest resolution: 2 Å / Lowest resolution: 25 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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