[English] 日本語
Yorodumi
- PDB-3owl: Human CK2 catalytic domain in complex with a benzopyridoindole de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3owl
TitleHuman CK2 catalytic domain in complex with a benzopyridoindole derivative inhibitor
ComponentsCSNK2A1 protein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SERINE/THREONINE-PROTEIN KINASE / CK2 / inhibitor / pyridocarbazol / ellipticine / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / : / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / rhythmic process / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 ...Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-19E / Casein kinase II subunit alpha / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsReiser, J.-B. / Prudent, R. / Cochet, C.
CitationJournal: Cancer Res. / Year: 2010
Title: Antitumor activity of pyridocarbazole and benzopyridoindole derivatives that inhibit protein kinase CK2.
Authors: Prudent, R. / Moucadel, V. / Nguyen, C.H. / Barette, C. / Schmidt, F. / Florent, J.C. / Lafanechere, L. / Sautel, C.F. / Duchemin-Pelletier, E. / Spreux, E. / Filhol, O. / Reiser, J.B. / Cochet, C.
History
DepositionSep 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CSNK2A1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2215
Polymers39,6501
Non-polymers5714
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.016, 46.012, 64.130
Angle α, β, γ (deg.)90.00, 111.69, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CSNK2A1 protein


Mass: 39650.223 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5U5J2, UniProt: P68400*PLUS
#2: Chemical ChemComp-19E / 11-chloro-8-methyl-7H-benzo[e]pyrido[4,3-b]indol-3-ol


Mass: 282.724 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11ClN2O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 36% polyethylene glycol 5000 monomethyl ether, 150 mM ammonium sulfate and 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→59.6 Å / Num. all: 18672 / Num. obs: 18672 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 24.07 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1744 / Rsym value: 0.402 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0088refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→59.59 Å / Cor.coef. Fo:Fc: 0.937 / SU B: 5.263 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26856 1906 10.2 %RANDOM
Rwork0.20439 ---
all0.20828 18672 --
obs0.20828 18672 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.987 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å2-0.42 Å2
2--2.23 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→59.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 35 114 2937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222914
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.963950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58223.121157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33915511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9331525
X-RAY DIFFRACTIONr_chiral_restr0.0940.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212249
X-RAY DIFFRACTIONr_mcbond_it0.7151.51655
X-RAY DIFFRACTIONr_mcangle_it1.28122693
X-RAY DIFFRACTIONr_scbond_it1.69331259
X-RAY DIFFRACTIONr_scangle_it2.6244.51255
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 149 -
Rwork0.252 1368 -
obs-1368 99.71 %

+
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