[English] 日本語
Yorodumi
- PDB-5ok3: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ok3
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp241 and Fasudil
Components
  • UPF0418 protein FAM164A
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / Complex / peptidic ligand / adamantyle
Function / homology
Function and homology information


cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cellular response to cold / regulation of osteoblast differentiation ...cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE / UPF0418 protein FAM164A / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.588 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Loewe-Corporation Germany
CitationJournal: Chemmedchem / Year: 2019
Title: Diamondoid Amino Acid-Based Peptide Kinase A Inhibitor Analogues.
Authors: Muller, J. / Kirschner, R.A. / Berndt, J.P. / Wulsdorf, T. / Metz, A. / Hrdina, R. / Schreiner, P.R. / Geyer, A. / Klebe, G.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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 / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
D: UPF0418 protein FAM164A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5623
Polymers43,2712
Non-polymers2911
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint6 kcal/mol
Surface area16950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.609, 73.281, 108.428
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 41193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cAMP-dependent protein kinase catalytic subunit alpha
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Tissue: Ovary / Gene: PRKACA / Organ: Ovary
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide UPF0418 protein FAM164A


Mass: 2077.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PKI 5-22 with T6ADA mutation / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48
#3: Chemical ChemComp-M77 / 5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE / Fasudil / (5-ISOQUINOLINESULFONYL)HOMOPIPERAZINE


Mass: 291.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O2S / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 5 mM Mes-Bis-Tris, 75 mM lithium chloride,1 mM DTT, 0.1 mM sodium EDTA, 0,25 mM Mega 8, 0.7 mM peptidic ligand, 5 mM Fasudil x HCl, 20 % v/v methanol/water in reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.886 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.59→45.771 Å / Num. obs: 63596 / % possible obs: 99.7 % / Redundancy: 7.34 % / CC1/2: 1 / Rsym value: 0.039 / Net I/σ(I): 26.22
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 7.51 % / Mean I/σ(I) obs: 3.14 / Num. unique obs: 9999 / CC1/2: 0.906 / Rsym value: 0.508 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.588→45.771 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 3180 5 %Random selection
Rwork0.1395 ---
obs0.1411 63594 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.588→45.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 20 289 3271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083123
X-RAY DIFFRACTIONf_angle_d0.9474252
X-RAY DIFFRACTIONf_dihedral_angle_d15.4461854
X-RAY DIFFRACTIONf_chiral_restr0.056448
X-RAY DIFFRACTIONf_plane_restr0.007560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5876-1.61130.28051280.16872438X-RAY DIFFRACTION94
1.6113-1.63650.22981380.15062616X-RAY DIFFRACTION100
1.6365-1.66330.1971350.13992576X-RAY DIFFRACTION100
1.6633-1.6920.21121360.12812583X-RAY DIFFRACTION100
1.692-1.72280.18841390.12262627X-RAY DIFFRACTION100
1.7228-1.75590.18461360.11892596X-RAY DIFFRACTION100
1.7559-1.79180.17121380.11452615X-RAY DIFFRACTION100
1.7918-1.83070.17521370.11412606X-RAY DIFFRACTION100
1.8307-1.87330.17741370.12172607X-RAY DIFFRACTION100
1.8733-1.92020.17871370.12672606X-RAY DIFFRACTION100
1.9202-1.97210.17161380.11982623X-RAY DIFFRACTION100
1.9721-2.03010.17431370.12382603X-RAY DIFFRACTION100
2.0301-2.09560.17571390.12422630X-RAY DIFFRACTION100
2.0956-2.17050.1661380.12162633X-RAY DIFFRACTION100
2.1705-2.25740.14081370.11582604X-RAY DIFFRACTION100
2.2574-2.36020.17661390.1242637X-RAY DIFFRACTION100
2.3602-2.48460.17821380.12712612X-RAY DIFFRACTION100
2.4846-2.64020.15881390.13222650X-RAY DIFFRACTION100
2.6402-2.84410.16771400.14492657X-RAY DIFFRACTION100
2.8441-3.13020.20171400.15412661X-RAY DIFFRACTION100
3.1302-3.5830.16911410.15622668X-RAY DIFFRACTION100
3.583-4.51360.15391430.14152731X-RAY DIFFRACTION100
4.5136-45.78980.16521500.15992835X-RAY DIFFRACTION100

+
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