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- PDB-5g6v: Crystal structure of the PCTAIRE1 kinase in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 5g6v
TitleCrystal structure of the PCTAIRE1 kinase in complex with inhibitor
ComponentsCYCLIN-DEPENDENT KINASE 16
KeywordsTRANSFERASE
Function / homology
Function and homology information


: / growth hormone secretion / regulation of insulin secretion involved in cellular response to glucose stimulus / exocytosis / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / positive regulation of autophagy / cytoplasmic side of plasma membrane / neuron projection development ...: / growth hormone secretion / regulation of insulin secretion involved in cellular response to glucose stimulus / exocytosis / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / positive regulation of autophagy / cytoplasmic side of plasma membrane / neuron projection development / microtubule cytoskeleton / synaptic vesicle / spermatogenesis / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Haspin like kinase domain / 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 ...Haspin like kinase domain / 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-919 / Cyclin-dependent kinase 16
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDixon-Clarke, S.E. / Galan Bartual, S. / Elkins, J. / Savitsky, P. / Kopec, J. / Mackenzie, A. / Tallant, C. / Heroven, C. / Burgess-Brown, N. / von Delft, F. ...Dixon-Clarke, S.E. / Galan Bartual, S. / Elkins, J. / Savitsky, P. / Kopec, J. / Mackenzie, A. / Tallant, C. / Heroven, C. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: Biochem.J. / Year: 2017
Title: Structure and inhibitor specificity of the PCTAIRE-family kinase CDK16.
Authors: Dixon-Clarke, S.E. / Shehata, S.N. / Krojer, T. / Sharpe, T.D. / von Delft, F. / Sakamoto, K. / Bullock, A.N.
History
DepositionAug 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_status / struct_ncs_dom_lim / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE 16
B: CYCLIN-DEPENDENT KINASE 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9738
Polymers74,6182
Non-polymers1,3556
Water4,720262
1
A: CYCLIN-DEPENDENT KINASE 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9874
Polymers37,3091
Non-polymers6783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYCLIN-DEPENDENT KINASE 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9874
Polymers37,3091
Non-polymers6783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.190, 86.940, 146.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA162 - 3031 - 142
21METMETBB162 - 3031 - 142
12VALVALAA323 - 474162 - 313
22VALVALBB323 - 474162 - 313

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.748912, -0.61252, 0.252883), (-0.615601, 0.501814, -0.607633), (0.245287, -0.610739, -0.752883)127.13885, 76.45946, 60.71938

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Components

#1: Protein CYCLIN-DEPENDENT KINASE 16 / / CDK16 / CELL DIVISION PROTEIN KINASE 16 / PCTAIRE-MOTIF PROTEIN KINASE 1 / SERINE/THREONINE-PROTEIN ...CDK16 / CELL DIVISION PROTEIN KINASE 16 / PCTAIRE-MOTIF PROTEIN KINASE 1 / SERINE/THREONINE-PROTEIN KINASE PCTAIRE-1


Mass: 37308.789 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 163-478 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q00536, cyclin-dependent kinase
#2: Chemical ChemComp-919 / 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide / DCC-2036


Mass: 553.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H28FN7O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsENGINEERED S319D PHOSPHO-MIMETIC MUTATION

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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: 2.44 Å3/Da / Density % sol: 49.51 % / Description: NONE
Crystal growpH: 5.5
Details: 25% PEG MEDIUM SMEAR (PEG 2000, PEG 3350, PEG 4000, PEG 5000MME) AND 0.1 M CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.91742
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91742 Å / Relative weight: 1
ReflectionResolution: 2.2→28.98 Å / Num. obs: 37175 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.4

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Processing

SoftwareName: REFMAC / Version: 5.8.0155 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→86.94 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.587 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1816 4.9 %RANDOM
Rwork0.20785 ---
obs0.21098 35328 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.421 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å20 Å2
2--0.69 Å2-0 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.2→86.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 98 262 5172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195017
X-RAY DIFFRACTIONr_bond_other_d0.0020.024760
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9666808
X-RAY DIFFRACTIONr_angle_other_deg0.9222.98710915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4425606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.82924.099222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95615841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4641525
X-RAY DIFFRACTIONr_chiral_restr0.0740.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215619
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021138
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1934.0832436
X-RAY DIFFRACTIONr_mcbond_other2.1924.0812435
X-RAY DIFFRACTIONr_mcangle_it3.5726.1113038
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1454.1962581
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 4495 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.630.5
2Bmedium thermal5.822
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 117 -
Rwork0.276 2570 -
obs--97.89 %

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