[English] 日本語
Yorodumi
- PDB-5lvm: Human PDK1 Kinase Domain in Complex with Adenine Bound to the ATP... -

+
Open data


ID or keywords:

Loading...

-
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


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 / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / 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 / phospholipase binding / GPVI-mediated activation cascade / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 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 / calcium-mediated signaling / negative regulation of transforming growth factor beta receptor signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / epidermal growth factor receptor signaling pathway / 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 / 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 / cytoplasm / cytosol
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

-
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)35,6803
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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