[English] 日本語
Yorodumi
- PDB-2izt: Structure of casein kinase gamma 3 in complex with inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2izt
TitleStructure of casein kinase gamma 3 in complex with inhibitor
ComponentsCASEIN KINASE I ISOFORM GAMMA-3
KeywordsTRANSFERASE / RANSFERASE / NUCLEOTIDE-BINDING / WNT SIGNALING PATHWAY
Function / homology
Function and homology information


protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding ...protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / 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 ...Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / 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-23D / Casein kinase I isoform gamma-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBunkoczi, G. / Salah, E. / Rellos, P. / Das, S. / Fedorov, O. / Savitsky, P. / Debreczeni, J.E. / Gileadi, O. / Sundstrom, M. / Edwards, A. ...Bunkoczi, G. / Salah, E. / Rellos, P. / Das, S. / Fedorov, O. / Savitsky, P. / Debreczeni, J.E. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / von Delft, F. / Knapp, S.
CitationJournal: To be Published
Title: Inhibitor Binding by Casein Kinases
Authors: Bunkoczi, G. / Salah, E. / Rellos, P. / Das, S. / Fedorov, O. / Savitsky, P. / Debreczeni, J.E. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / von Delft, F. / Knapp, S.
History
DepositionJul 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CASEIN KINASE I ISOFORM GAMMA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0144
Polymers38,5571
Non-polymers4573
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.433, 56.433, 220.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein CASEIN KINASE I ISOFORM GAMMA-3 / CKI-GAMMA 3 / CASEIN KINASE 1 GAMMA 3


Mass: 38557.395 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y6M4, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-23D / N2-[(1R,2S)-2-AMINOCYCLOHEXYL]-N6-(3-CHLOROPHENYL)-9-ETHYL-9H-PURINE-2,6-DIAMINE


Mass: 385.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24ClN7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCASEIN KINASES ARE OPERATIONALLY DEFINED BY THEIR PREFERENTIAL UTILIZATION OF ACIDIC PROTEINS SUCH ...CASEIN KINASES ARE OPERATIONALLY DEFINED BY THEIR PREFERENTIAL UTILIZATION OF ACIDIC PROTEINS SUCH AS CASEINS AS SUBSTRATES.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 8
Details: 0.05 M CACL2, 20% PEG6000, 10% ETHYLENE GLYCOL, 0.10 M TRIS PH=8.0, pH 8.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 10, 2006
RadiationMonochromator: OSMIC HR MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→32.7 Å / Num. obs: 26655 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 87.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CHL

2chl


Resolution: 2→29.35 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.872 / SU B: 10.918 / SU ML: 0.163 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1333 5.1 %RANDOM
Rwork0.222 ---
obs0.225 24862 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 23 246 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222572
X-RAY DIFFRACTIONr_bond_other_d0.0020.021818
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9893476
X-RAY DIFFRACTIONr_angle_other_deg0.98134396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1425302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14322.846123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70415457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5951521
X-RAY DIFFRACTIONr_chiral_restr0.0840.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022821
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02566
X-RAY DIFFRACTIONr_nbd_refined0.1990.2628
X-RAY DIFFRACTIONr_nbd_other0.2070.22105
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21248
X-RAY DIFFRACTIONr_nbtor_other0.0890.21406
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1531540
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.04252434
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.13181188
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.39111041
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.445 80
Rwork0.386 1634
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9171-1.05421.3882.4847-1.18622.1731-0.01960.23370.11530.097-0.2088-0.2092-0.08810.16970.2284-0.1521-0.0044-0.0260.06110.0164-0.006345.2771-10.678828.7121
21.30260.0945-0.2690.9056-0.29711.3444-0.00380.0751-0.0708-0.1221-0.04840.0015-0.0078-0.00610.0522-0.0988-0.0061-0.0047-0.0302-0.0145-0.090425.2051-5.697715.7053
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 107
2X-RAY DIFFRACTION2A108 - 322

+
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