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- PDB-4aaa: Crystal structure of the human CDKL2 kinase domain -

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Basic information

Entry
Database: PDB / ID: 4aaa
TitleCrystal structure of the human CDKL2 kinase domain
ComponentsCYCLIN-DEPENDENT KINASE-LIKE 2
KeywordsTRANSFERASE / PHOSPHO-MIMETIC
Function / homology
Function and homology information


sex differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / signal transduction / nucleoplasm / ATP binding ...sex differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / signal transduction / nucleoplasm / 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 ...: / 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-DKI / Cyclin-dependent kinase-like 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsCanning, P. / Vollmar, M. / Cooper, C.D.O. / Mahajan, P. / Daga, N. / Berridge, G. / Burgess-Brown, N. / Muniz, J.R.C. / Krojer, T. / von Delft, F. ...Canning, P. / Vollmar, M. / Cooper, C.D.O. / Mahajan, P. / Daga, N. / Berridge, G. / Burgess-Brown, N. / Muniz, J.R.C. / Krojer, T. / von Delft, F. / Weigelt, J. / 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, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Mar 30, 2022Group: Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_status / 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 / _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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1888
Polymers38,3901
Non-polymers7987
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.819, 70.220, 83.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYCLIN-DEPENDENT KINASE-LIKE 2 / PROTEIN KINASE P56 KKIAMRE / SERINE/THREONINE-PROTEIN KINASE KKIAMRE


Mass: 38390.457 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-308 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HIS85 CONFORMATION B AND ASP84 CONFORMATION A MAY NOT BE OCCUPIED SIMULTANEOUSLY.
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q92772, cyclin-dependent kinase
#2: Chemical ChemComp-DKI / 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE / CDK 1/2 INHIBITOR


Mass: 425.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F2N7O2S2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 159 TO ASP ENGINEERED RESIDUE IN CHAIN A, TYR 161 TO GLU
Nonpolymer details5-AMINO-3-((4-(AMINOSULFONYL)PHENYL)AMINO)-N-(2, 6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1- ...5-AMINO-3-((4-(AMINOSULFONYL)PHENYL)AMINO)-N-(2, 6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE (DKI): CDK12 INHIBITOR III
Sequence detailsTWO PHOSPHO-MIMETIC ACTIVATING MUTATIONS INTRODUCED.

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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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE
Crystal growDetails: 0.2M NACL, 0.1M TRIS PH 8.5; 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→42.14 Å / Num. obs: 53461 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NIZ

3niz


Resolution: 1.53→53.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.88 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED. RESIDUES 149 TO 160 ARE DISORDERED RESIDUE HIS85 CONFORMATION B AND ASP84 CONFORMATION A MAY NOT BE OCCUPIED SIMULTANEOUSLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 3041 5.1 %RANDOM
Rwork0.18033 ---
obs0.18178 56974 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.666 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--1.14 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.53→53.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 52 259 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022639
X-RAY DIFFRACTIONr_bond_other_d0.0010.021865
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9763576
X-RAY DIFFRACTIONr_angle_other_deg0.9352.9974554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5095331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51824.286133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98115495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.581517
X-RAY DIFFRACTIONr_chiral_restr0.0980.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
X-RAY DIFFRACTIONr_nbd_refined0.2750.2797
X-RAY DIFFRACTIONr_nbd_other0.1780.21838
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21259
X-RAY DIFFRACTIONr_nbtor_other0.0880.21258
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.24
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
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11
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: 1.533→1.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 174 -
Rwork0.395 3479 -
obs--86.63 %
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)
10.28650.16490.32670.22960.37610.65760.02410.0941-0.188-0.0020.0841-0.0286-0.0330.1439-0.10830.0637-0.0036-0.00310.0487-0.04980.175329.6913-0.341878.4371
21.60670.4730.32040.39980.16240.0824-0.0520.3794-0.38010.10830.1173-0.08110.01920.0788-0.06530.073-0.02220.01120.1328-0.07980.113242.16591.506378.6955
30.4510.22570.00440.3923-0.08890.03120.0219-0.0450.0161-0.0198-0.02450.00270.0174-0.00360.00260.0494-0.00320.00210.0467-0.00440.03834.994821.43580.3436
40.1987-0.02790.06590.1512-0.15530.8190.00820.01550.07050.0115-0.0449-0.0142-0.02220.01560.03680.041-0.0063-0.00420.04790.01820.034342.703632.900273.0624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 34
2X-RAY DIFFRACTION2A35 - 85
3X-RAY DIFFRACTION3A86 - 165
4X-RAY DIFFRACTION4A166 - 303

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