[English] 日本語
Yorodumi
- PDB-2jdo: STRUCTURE OF PKB-BETA (AKT2) COMPLEXED WITH ISOQUINOLINE-5-SULFON... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jdo
TitleSTRUCTURE OF PKB-BETA (AKT2) COMPLEXED WITH ISOQUINOLINE-5-SULFONIC ACID (2-(2-(4-CHLOROBENZYLOXY) ETHYLAMINO)ETHYL)AMIDE
Components
  • GLYCOGEN SYNTHASE KINASE-3 BETA
  • RAC-BETA SERINE/THREONINE-PROTEIN KINASE
KeywordsTRANSFERASE / WNT SIGNALING PATHWAY / SERINE/THREONINE-PROTEIN KINASE / KINASE / ATP-BINDING / PHOSPHORYLATION / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING
Function / homology
Function and homology information


PDE3B signalling / Inhibition of TSC complex formation by AKT (PKB) / positive regulation of cap-dependent translational initiation / AKT-mediated inactivation of FOXO1A / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / Activation of AKT2 / mammary gland epithelial cell differentiation / AKT phosphorylates targets in the nucleus / negative regulation of glycogen (starch) synthase activity ...PDE3B signalling / Inhibition of TSC complex formation by AKT (PKB) / positive regulation of cap-dependent translational initiation / AKT-mediated inactivation of FOXO1A / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / Activation of AKT2 / mammary gland epithelial cell differentiation / AKT phosphorylates targets in the nucleus / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / negative regulation of type B pancreatic cell development / regulation of protein export from nucleus / superior temporal gyrus development / cellular response to interleukin-3 / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / positive regulation of fatty acid beta-oxidation / positive regulation of glucose metabolic process / negative regulation of TORC2 signaling / RUNX2 regulates genes involved in cell migration / beta-arrestin-dependent dopamine receptor signaling pathway / negative regulation of dopaminergic neuron differentiation / positive regulation of protein localization to centrosome / maintenance of cell polarity / positive regulation of cell motility / positive regulation of cilium assembly / regulation of long-term synaptic potentiation / heart valve development / tau-protein kinase / CRMPs in Sema3A signaling / beta-catenin destruction complex / RAB GEFs exchange GTP for GDP on RABs / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / glycogen biosynthetic process / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of calcineurin-NFAT signaling cascade / Maturation of nucleoprotein / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / negative regulation of TOR signaling / positive regulation of cell-matrix adhesion / regulation of microtubule-based process / Wnt signalosome / AKT phosphorylates targets in the cytosol / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of axon extension / positive regulation of protein binding / regulation of neuron projection development / negative regulation of protein localization to nucleus / Maturation of nucleoprotein / glycogen metabolic process / Regulation of TP53 Activity through Association with Co-factors / ER overload response / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / regulation of axonogenesis / Co-inhibition by CTLA4 / establishment of cell polarity / negative regulation of PERK-mediated unfolded protein response / regulation of dendrite morphogenesis / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / canonical Wnt signaling pathway / Regulation of MITF-M-dependent genes involved in pigmentation / Regulation of localization of FOXO transcription factors / extrinsic apoptotic signaling pathway in absence of ligand / dynactin binding / epithelial to mesenchymal transition / CD28 dependent PI3K/Akt signaling / Activation of BAD and translocation to mitochondria / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Regulation of HSF1-mediated heat shock response / positive regulation of blood vessel endothelial cell migration / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of glycogen biosynthetic process / positive regulation of protein targeting to membrane / fat cell differentiation / negative regulation of osteoblast differentiation / extrinsic apoptotic signaling pathway / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / NF-kappaB binding / Cyclin E associated events during G1/S transition / negative regulation of protein-containing complex assembly / cellular response to retinoic acid / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / regulation of cellular response to heat / positive regulation of protein export from nucleus / positive regulation of type I interferon production / positive regulation of D-glucose import across plasma membrane / presynaptic modulation of chemical synaptic transmission
Similarity search - Function
Protein Kinase B beta, catalytic domain / Protein Kinase B, pleckstrin homology domain / Glycogen synthase kinase 3, catalytic domain / : / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain ...Protein Kinase B beta, catalytic domain / Protein Kinase B, pleckstrin homology domain / Glycogen synthase kinase 3, catalytic domain / : / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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
Chem-I5S / RAC-beta serine/threonine-protein kinase / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.8 Å
AuthorsDavies, T.G. / Verdonk, M.L. / Graham, B. / Saalau-Bethell, S. / Hamlett, C.C.F. / Mchardy, T. / Collins, I. / Garrett, M.D. / Workman, P. / Woodhead, S.J. ...Davies, T.G. / Verdonk, M.L. / Graham, B. / Saalau-Bethell, S. / Hamlett, C.C.F. / Mchardy, T. / Collins, I. / Garrett, M.D. / Workman, P. / Woodhead, S.J. / Jhoti, H. / Barford, D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A Structural Comparison of Inhibitor Binding to Pkb, Pka and Pka-Pkb Chimera
Authors: Davies, T.G. / Verdonk, M.L. / Graham, B. / Saalau-Bethell, S. / Hamlett, C.C.F. / Mchardy, T. / Collins, I. / Garrett, M.D. / Workman, P. / Woodhead, S.J. / Jhoti, H. / Barford, D.
History
DepositionJan 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAC-BETA SERINE/THREONINE-PROTEIN KINASE
C: GLYCOGEN SYNTHASE KINASE-3 BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4664
Polymers40,9842
Non-polymers4822
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.262, 60.700, 132.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RAC-BETA SERINE/THREONINE-PROTEIN KINASE / PROTEIN KINASE B-BETA / RAC-PK-BETA / PROTEIN KINASE AKT-2 / PROTEIN KINASE B / BETA / PKB BETA


Mass: 39860.383 Da / Num. of mol.: 1 / Fragment: KINASE CATALYTIC DOMAIN, RESIDUES 146-467
Source method: isolated from a genetically manipulated source
Details: PIFTIDE SEQUENCE (EEQEMFEDFDYIADW) REPLACES NATURAL PKB SEQUENCE AFTER RESIDUE 464
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P31751, non-specific serine/threonine protein kinase
#2: Protein/peptide GLYCOGEN SYNTHASE KINASE-3 BETA / GSK3-BETA PEPTIDE / GSK-3 BETA


Mass: 1123.220 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-12 / Source method: obtained synthetically / Details: PEPTIDE DERIVED FROM THE KINASE GSK3-BETA / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P49841, tau-protein kinase
#3: Chemical ChemComp-I5S / ISOQUINOLINE-5-SULFONIC ACID (2-(2-(4-CHLOROBENZYLOXY)ETHYLAMINO)ETHYL)AMIDE


Mass: 419.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22ClN3O3S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCLONE DOES NOT CONTAIN THE FIRST 145 RESIDUES OF THE P31751 SEQUENCE (PH-DOMAIN). RESIDUES GAMDP AT ...CLONE DOES NOT CONTAIN THE FIRST 145 RESIDUES OF THE P31751 SEQUENCE (PH-DOMAIN). RESIDUES GAMDP AT THE START OF THE CLONED SEQUENCE ARE ARTEFACTS FROM A PURIFICATION TAG, HOWEVER THESE ARE NOT VISIBLE IN THE STRUCTURE AND WERE NOT BUILT. THE CLONE CONTAINS THE SEQUENCE EEQEMFEDFDYIADW (PIFTIDE) INSTEAD OF THE P31751 SEQUENCE FROM POSITION 465 ONWARDS. RESIDUES 450 - 468 ARE DISORDERED AND HAVE NOT BEEN BUILT IN THE STRUCTURE. RESIDUES 3-12 ONLY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.46 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→55 Å / Num. obs: 31145 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.4

-
Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.8→55.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.454 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1676 5.1 %RANDOM
Rwork0.175 ---
obs0.177 31145 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---1.22 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→55.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 32 323 3021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222760
X-RAY DIFFRACTIONr_bond_other_d0.0010.021937
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9623719
X-RAY DIFFRACTIONr_angle_other_deg0.8262.9844672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5575322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00823.285137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26715.222495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9711522
X-RAY DIFFRACTIONr_chiral_restr0.0680.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023021
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02610
X-RAY DIFFRACTIONr_nbd_refined0.2040.2531
X-RAY DIFFRACTIONr_nbd_other0.1870.22044
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21340
X-RAY DIFFRACTIONr_nbtor_other0.080.21370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0860.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.06151615
X-RAY DIFFRACTIONr_mcbond_other0.0255656
X-RAY DIFFRACTIONr_mcangle_it0.0962604
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.07861145
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1097.51115
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 93 -
Rwork0.205 1764 -
obs--72.97 %

+
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