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- PDB-6z2v: CLK3 A319V mutant bound with beta-carboline KH-CARB13 (Cpd 3) -

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Basic information

Entry
Database: PDB / ID: 6z2v
TitleCLK3 A319V mutant bound with beta-carboline KH-CARB13 (Cpd 3)
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / Inhibitor / Complex / CLK3 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / protein phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / protein phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane
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-KHC / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchroeder, M. / Chaikuad, A. / Bracher, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: DFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity.
Authors: Schroder, M. / Bullock, A.N. / Fedorov, O. / Bracher, F. / Chaikuad, A. / Knapp, S.
History
DepositionMay 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.2Jan 24, 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 CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8114
Polymers42,3461
Non-polymers4643
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint3 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.376, 45.393, 106.334
Angle α, β, γ (deg.)90.000, 111.160, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Dual specificity protein kinase CLK3 / CDC-like kinase 3


Mass: 42346.465 Da / Num. of mol.: 1 / Mutation: A319V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Production host: Escherichia coli (E. coli) / References: UniProt: P49761, dual-specificity kinase
#2: Chemical ChemComp-KHC / (4~{S})-7,8-bis(chloranyl)-9-methyl-1-oxidanylidene-spiro[2,4-dihydropyrido[3,4-b]indole-3,4'-piperidine]-4-carbonitrile


Mass: 363.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16Cl2N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24% PEG 3350, 0,2M KSCN, 10% Ethylene Glycol, 0.1M bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→39.37 Å / Num. obs: 11812 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.985 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.101 / Rrim(I) all: 0.266 / Net I/σ(I): 6.4
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
2.6-2.727.21.3191037814410.5970.5271.4221.6100
9.01-39.346.70.09620863120.990.040.10416.298.9

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2eu9

2eu9


Resolution: 2.6→39.37 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.884 / SU B: 32.769 / SU ML: 0.332 / SU R Cruickshank DPI: 0.2962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 559 4.7 %RANDOM
Rwork0.2019 ---
obs0.2051 11251 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.95 Å2 / Biso mean: 35.266 Å2 / Biso min: 8.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0.91 Å2
2--1.06 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 2.6→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 29 61 2833
Biso mean--60.08 27.06 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132866
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172584
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.6443883
X-RAY DIFFRACTIONr_angle_other_deg1.331.5825971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7795341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51821.79162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51715479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2781519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023276
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02646
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 50 -
Rwork0.314 835 -
all-885 -
obs--100 %
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)
15.2859-2.17281.36946.1735-0.7262.46910.0276-0.1319-0.02730.5351-0.1334-0.4385-0.02020.41870.10580.1807-0.0961-0.04130.25180.0110.140791.2059.38386.197
22.8616-0.0219-0.17881.93020.27080.973-0.01620.08220.12310.02680.040.0629-0.01990.0601-0.02380.01960.0044-0.03570.0089-0.00840.080167.38611.24595.824
32.6788-0.9066-0.28585.61691.89534.03930.1385-0.07840.33190.1151-0.04910.4423-0.38270.0679-0.08940.0663-0.00940.04830.0796-0.05240.306654.73518.83398.983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 203
2X-RAY DIFFRACTION2A204 - 419
3X-RAY DIFFRACTION3A420 - 480

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