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- PDB-2izr: Structure of casein kinase gamma 3 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2izr
TitleStructure of casein kinase gamma 3 in complex with inhibitor
ComponentsCASEIN KINASE I ISOFORM GAMMA-3
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / KINASE / ATP-BINDING / PHOSPHORYLATION / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING / WNT SIGNALING PATHWAY / SERINE/THREONINE KINASE
Function / homology
Function and homology information


protein modification process / endocytosis / positive regulation of canonical Wnt signaling pathway / protein kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / 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-BRK / S-1,2-PROPANEDIOL / Casein kinase I isoform gamma-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,1799
Polymers38,5571
Non-polymers6228
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.724, 56.724, 223.344
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#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 BL21(DE3) (bacteria)
References: UniProt: Q9Y6M4, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 482 molecules

#2: Chemical ChemComp-BRK / {(2Z)-4-AMINO-2-[(4-METHOXYPHENYL)IMINO]-2,3-DIHYDRO-1,3-THIAZOL-5-YL}(4-METHOXYPHENYL)METHANONE


Mass: 355.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17N3O3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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Details

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.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7
Details: 10% PEG10K, 0.20 M MGCL2, 0.1 M TRIS PH=7.0, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978978
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 4, 2006 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978978 Å / Relative weight: 1
ReflectionResolution: 1.3→49.1 Å / Num. obs: 99653 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.4
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.8 / % possible all: 79.7

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Processing

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

2chl


Resolution: 1.3→49.15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.262 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.158 4952 5 %RANDOM
Rwork0.13 ---
obs0.132 94592 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å20 Å2
2---0.23 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.3→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 36 474 2923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222609
X-RAY DIFFRACTIONr_bond_other_d0.0010.021827
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9933529
X-RAY DIFFRACTIONr_angle_other_deg0.9183.0014437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2323.415123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33115471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0681518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
X-RAY DIFFRACTIONr_nbd_refined0.2240.2541
X-RAY DIFFRACTIONr_nbd_other0.1930.21885
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21278
X-RAY DIFFRACTIONr_nbtor_other0.0840.21256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2334
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.17531591
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.27452479
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.93981197
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.115111050
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: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 257
Rwork0.21 4878

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