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- PDB-3zdu: Crystal structure of the human CDKL3 kinase domain -

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Basic information

Entry
Database: PDB / ID: 3zdu
TitleCrystal structure of the human CDKL3 kinase domain
ComponentsCYCLIN-DEPENDENT KINASE-LIKE 3
KeywordsTRANSFERASE / PHOSPHO-MIMETIC
Function / homology
Function and homology information


dendrite extension / protein modification process => GO:0036211 / negative regulation of axon extension / positive regulation of dendrite morphogenesis / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / protein kinase activity / protein phosphorylation / ATP binding / nucleus / cytoplasm
Similarity search - Function
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. ...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-38R / Cyclin-dependent kinase-like 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCanning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Pike, A.C.W. / Quigley, A. / MacKenzie, A. / Carpenter, E.P. / von Delft, F. / Arrowsmith, C.H. ...Canning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Pike, A.C.W. / Quigley, A. / MacKenzie, A. / Carpenter, E.P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: Cell Rep / Year: 2018
Title: CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function.
Authors: Canning, P. / Park, K. / Goncalves, J. / Li, C. / Howard, C.J. / Sharpe, T.D. / Holt, L.J. / Pelletier, L. / Bullock, A.N. / Leroux, M.R.
History
DepositionNov 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Mar 30, 2022Group: Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE-LIKE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9897
Polymers37,3511
Non-polymers6376
Water2,864159
1
A: CYCLIN-DEPENDENT KINASE-LIKE 3
hetero molecules

A: CYCLIN-DEPENDENT KINASE-LIKE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,97814
Polymers74,7032
Non-polymers1,27512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2840 Å2
ΔGint-152.7 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.930, 63.930, 163.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2079-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYCLIN-DEPENDENT KINASE-LIKE 3 / SERINE/THREONINE-PROTEIN KINASE NKIAMRE


Mass: 37351.379 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-324 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: TWO PHOSPHOMIMETIC POINT MUTATIONS INTRODUCED, T158D AND Y160E
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SITE-DIRECTED MUTAGENESIS / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8IVW4, cyclin-dependent kinase

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Non-polymers , 5 types, 165 molecules

#2: Chemical ChemComp-38R / [4-({4-[(3-cyclopentyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile


Mass: 359.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details38R: ATP-MIMETIC KINASE INHIBITOR ASC67

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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: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE
Crystal growDetails: 0.03M ZN CL, 30% PEG_6000, 5% ETHYLENE GLYCOL, MES PH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.2→54.54 Å / Num. obs: 20446 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENSEMBLE OF PDB ENTRIES 4AGU AND 4AAA

4agu

4aaa


Resolution: 2.2→45.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / SU B: 12.919 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26248 1013 5.1 %RANDOM
Rwork0.21425 ---
obs0.21662 18821 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.118 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å21.27 Å20 Å2
2--1.27 Å20 Å2
3----4.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 38 159 2516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192414
X-RAY DIFFRACTIONr_bond_other_d0.0010.022298
X-RAY DIFFRACTIONr_angle_refined_deg1.511.973261
X-RAY DIFFRACTIONr_angle_other_deg0.79335257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5545294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1523.861101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95615397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0661510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
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_it1.1431.9991185
X-RAY DIFFRACTIONr_mcbond_other1.1421.9971184
X-RAY DIFFRACTIONr_mcangle_it1.8232.9951476
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7632.1261227
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
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.7 50 -
Rwork0.628 1056 -
obs--75.55 %
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)
19.7144-7.11140.98558.6422-0.25170.2499-0.10240.4717-0.195-0.1274-0.10591.5142-0.0903-0.11030.20830.71060.2165-0.00440.48510.01540.584117.81925.551257.4661
21.76540.6072-0.28312.8234-1.47430.7605-0.62630.23420.1460.22120.92861.1553-0.9654-1.0206-0.30242.04691.51320.27411.55190.15270.426717.946216.733372.0421
30.9742-1.26241.31574.0969-0.12633.6202-0.1042-0.1322-0.02220.1730.19130.4565-0.5113-0.3617-0.08720.45450.08810.13380.20680.0270.237329.789916.526366.8983
42.55980.968-0.44224.8450.5162.8972-0.0688-0.0314-0.17250.08370.0981-0.14550.13440.0201-0.02940.19730.03590.01270.13590.01120.02837.5172-0.115769.6608
51.2484-0.1673-5.0580.9283-0.658622.5698-0.16970.0389-0.0340.66330.22540.2885-0.4309-0.5585-0.05570.75940.00320.01150.63470.01280.734236.152835.241470.9341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 34
2X-RAY DIFFRACTION2A35 - 60
3X-RAY DIFFRACTION3A61 - 159
4X-RAY DIFFRACTION4A160 - 302
5X-RAY DIFFRACTION5A303 - 309

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