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- PDB-7ak3: CLK1 bound with CAF052 -

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Basic information

Entry
Database: PDB / ID: 7ak3
TitleCLK1 bound with CAF052
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / CLK1 / Kinase / Inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
: / 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
Similarity search - Domain/homology
Chem-RH8 / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSchroeder, M. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Int J Mol Sci / Year: 2020
Title: Crystal Structure and Inhibitor Identifications Reveal Targeting Opportunity for the Atypical MAPK Kinase ERK3.
Authors: Schroder, M. / Filippakopoulos, P. / Schwalm, M.P. / Ferrer, C.A. / Drewry, D.H. / Knapp, S. / Chaikuad, A.
History
DepositionSep 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9862
Polymers39,5821
Non-polymers4041
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.022, 64.159, 78.529
Angle α, β, γ (deg.)90.000, 119.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

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Components

#1: Protein Dual specificity protein kinase CLK1 / CDC-like kinase 1


Mass: 39581.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Production host: Escherichia coli (E. coli) / References: UniProt: P49759, dual-specificity kinase
#2: Chemical ChemComp-RH8 / ~{N}-[3-fluoranyl-4-(4-methylpiperazin-1-yl)phenyl]-4-pyrazolo[1,5-b]pyridazin-3-yl-pyrimidin-2-amine


Mass: 404.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21FN8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 23% PEG 6000, 0.1 M bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→47.96 Å / Num. obs: 13502 / % possible obs: 98 % / Redundancy: 2.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.048 / Rrim(I) all: 0.078 / Net I/σ(I): 7.5 / Num. measured all: 31003 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.62.30.468353415270.880.3740.6031.898.1
9.01-47.962.20.0376492950.9940.0290.04718.594.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1z57

1z57


Resolution: 2.5→45.31 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 33.025 / SU ML: 0.317 / SU R Cruickshank DPI: 0.6554 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.655 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 689 5.1 %RANDOM
Rwork0.2108 ---
obs0.2134 12810 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.44 Å2 / Biso mean: 72.692 Å2 / Biso min: 50.93 Å2
Baniso -1Baniso -2Baniso -3
1--3.44 Å20 Å22.8 Å2
2---9.05 Å20 Å2
3---5.73 Å2
Refinement stepCycle: final / Resolution: 2.5→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2682 0 30 19 2731
Biso mean--54.5 68.6 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132792
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172506
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.6383792
X-RAY DIFFRACTIONr_angle_other_deg1.1611.5865796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64522.378143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06615458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2061514
X-RAY DIFFRACTIONr_chiral_restr0.0520.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 41 -
Rwork0.357 944 -
all-985 -
obs--97.43 %
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)
12.3176-0.0721-1.2481.91150.52462.4565-0.0257-0.01610.0299-0.0482-0.03710.2017-0.1213-0.01380.06280.02860.0272-0.01630.0392-0.0080.05117.961610.468222.4888
22.51420.8807-0.30952.37920.49383.794-0.21270.22360.0509-0.41940.0920.0401-0.11820.2530.12070.1038-0.01340.03460.0682-0.01040.154922.82371.02275.0905
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A147 - 338
2X-RAY DIFFRACTION2A339 - 483

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