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- PDB-4bbm: CRYSTAL STRUCTURE OF THE HUMAN CDKL2 KINASE DOMAIN WITH BOUND TCS 2312 -

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Basic information

Entry
Database: PDB / ID: 4bbm
TitleCRYSTAL STRUCTURE OF THE HUMAN CDKL2 KINASE DOMAIN WITH BOUND TCS 2312
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
: / 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 ...: / 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-TC0 / Cyclin-dependent kinase-like 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCanning, P. / Elkins, J.M. / Cooper, C.D.O. / Mahajan, P. / Daga, N. / Berridge, G. / Burgess-Brown, N. / Muniz, J.R.C. / Krojer, T. / Arrowsmith, C.H. ...Canning, P. / Elkins, J.M. / Cooper, C.D.O. / Mahajan, P. / Daga, N. / Berridge, G. / Burgess-Brown, N. / Muniz, J.R.C. / Krojer, T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / 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
DepositionSep 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: 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 / 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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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
B: CYCLIN-DEPENDENT KINASE-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,92510
Polymers76,7812
Non-polymers1,1448
Water3,423190
1
A: CYCLIN-DEPENDENT KINASE-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9635
Polymers38,3901
Non-polymers5724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYCLIN-DEPENDENT KINASE-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9635
Polymers38,3901
Non-polymers5724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.583, 68.047, 82.343
Angle α, β, γ (deg.)71.53, 89.92, 88.97
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: -3 - 308 / Label seq-ID: 20 - 331

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-1, 0.0014, 0.0052), (0.0021, -0.7901, 0.613), (0.0049, 0.613, 0.7901)
Vector: -9.8912, -9.7194, -40.2295)

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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.: 2 / Fragment: KINASE DOMAIN, RESIDUES 1-308 / Mutation: YES
Source method: isolated from a genetically manipulated source
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: Q92772, cyclin-dependent kinase
#2: Chemical ChemComp-TC0 / 4'-[5-[[3-[(CYCLOPROPYLAMINO)METHYL]PHENYL]AMINO]-1H-PYRAZOL-3-YL]-[1,1'-BIPHENYL]-2,4-DIOL


Mass: 412.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H24N4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details4'-[5-[[3-[(CYCLOPROPYLAMINO)METHYL] PHENYL]AMINO]-1H-PYRAZOL-3-YL]-[1,1'-BIPHENYL]-2,4- DIOL (TC0): ...4'-[5-[[3-[(CYCLOPROPYLAMINO)METHYL] PHENYL]AMINO]-1H-PYRAZOL-3-YL]-[1,1'-BIPHENYL]-2,4- DIOL (TC0): CHK1 INHIBITOR TC0 2312
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: 2.19 Å3/Da / Density % sol: 43.85 % / Description: NONE
Crystal growDetails: 0.2M (NH4)2SO4, 0.1M CACODYLATE PH 6.5, 30% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2→39.39 Å / Num. obs: 42854 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.4 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AAA

4aaa


Resolution: 2→39.39 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.301 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26896 2145 5 %RANDOM
Rwork0.24253 ---
obs0.24386 40614 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.105 Å2
Baniso -1Baniso -2Baniso -3
1--17.8 Å210.48 Å20.24 Å2
2--43.47 Å2-12.63 Å2
3----25.67 Å2
Refinement stepCycle: LAST / Resolution: 2→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 80 190 4956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194871
X-RAY DIFFRACTIONr_bond_other_d0.0040.024525
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9766604
X-RAY DIFFRACTIONr_angle_other_deg0.9273.00310331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69624.35223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46315764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5861524
X-RAY DIFFRACTIONr_chiral_restr0.0750.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215553
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021145
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 16597 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 173 -
Rwork0.356 2930 -
obs--96.85 %
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)
14.40931.31911.15231.5237-0.27593.983-0.14950.29820.0099-0.173-0.07250.01230.10840.07720.2220.4877-0.0155-0.01130.11760.16650.433-15.52287.4879-54.4641
21.1222-0.29560.34412.4726-0.51391.95820.00870.27380.2771-0.1608-0.0048-0.1398-0.19130.0892-0.00390.1229-0.01240.01720.07350.08370.1649-12.2148-0.8141-40.0824
30.7791.3054-0.87562.55410.10488.6326-0.15040.01560.1441-0.4505-0.17460.2647-0.4019-0.5620.3250.31540.13120.02570.30210.12660.229-6.6455-11.0728-51.7191
41.8207-0.6005-0.48921.65581.32563.3209-0.0621-0.1041-0.10580.08710.0440.03330.220.04880.01810.0838-0.0207-0.01810.02620.04420.0999-10.3013-18.3467-35.5364
51.76661.2575-1.69924.0403-0.35313.11210.01580.5032-0.3346-0.66150.09660.28330.2948-0.3175-0.11240.64320.1077-0.22780.42-0.05910.67014.135-22.31182.2053
61.596-0.11570.45883.0833-0.48552.4063-0.0517-0.1443-0.3276-0.09870.1470.08760.3398-0.0919-0.09520.1387-0.0114-0.01250.030.06190.15162.0974-5.1046.609
74.04260.76190.28080.56170.2340.14370.80320.3913-0.5190.0325-0.3309-0.56210.06160.1009-0.47240.77470.3215-0.20170.9842-0.10130.79911.9851-11.2866-9.6572
81.8732-0.21991.02150.88080.43734.22360.0042-0.05950.1322-0.09080.012-0.0185-0.1545-0.0281-0.01620.0854-0.00870.00840.01360.03110.1313-0.26968.6726-2.5048
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 59
2X-RAY DIFFRACTION2A60 - 143
3X-RAY DIFFRACTION3A144 - 168
4X-RAY DIFFRACTION4A169 - 308
5X-RAY DIFFRACTION5B-3 - 59
6X-RAY DIFFRACTION6B60 - 142
7X-RAY DIFFRACTION7B143 - 155
8X-RAY DIFFRACTION8B156 - 308

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