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- PDB-6z55: Crystal structure of CLK3 in complex with macrocycle ODS2004070 -

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Basic information

Entry
Database: PDB / ID: 6z55
TitleCrystal structure of CLK3 in complex with macrocycle ODS2004070
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / kinase / kinase inhibitor / clk3 / macrocycle / nanocyclic / 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 / nuclear speck / protein phosphorylation / 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 / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chem-PQ5 / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChaikuad, A. / Benderitter, P. / Hoflack, J. / Denis, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of CLK3 in complex with macrocycle ODS2004070
Authors: Chaikuad, A. / Benderitter, P. / Hoflack, J. / Denis, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionMay 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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: Dual specificity protein kinase CLK3
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,41337
Polymers84,6372
Non-polymers2,77635
Water16,718928
1
A: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,79720
Polymers42,3181
Non-polymers1,47819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,61617
Polymers42,3181
Non-polymers1,29816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.730, 131.360, 83.800
Angle α, β, γ (deg.)90.000, 107.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

PO4

21B-502-

PO4

31B-928-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 128 - 481 / Label seq-ID: 4 - 357

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

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 42318.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: P49761, dual-specificity kinase

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Non-polymers , 5 types, 963 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PQ5 / 7,10-Dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.12,6.017,20]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxylic acid


Mass: 340.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16N4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% PEG 3350, 0.2M potassium/sodium phosphate, 0.1M bis-tris-propane pH 7.0, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→79.788 Å / Num. all: 104048 / Num. obs: 104048 / % possible obs: 95.5 % / Redundancy: 4.5 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.083 / Rsym value: 0.073 / Net I/av σ(I): 7.5 / Net I/σ(I): 10.7 / Num. measured all: 469469
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.794.50.733169001153080.3820.830.733296.5
1.79-1.94.20.4681.657818137310.2530.5360.4682.891.2
1.9-2.034.60.2892.662091134900.1490.3260.2894.695.8
2.03-2.194.70.1764.360387129130.090.1980.1767.298.1
2.19-2.44.60.1226.154374118500.0630.1370.1229.897.8
2.4-2.694.20.0868.442798101900.0460.0990.08612.293.3
2.69-3.14.60.06211.14236892260.0320.070.06217.795.3
3.1-3.84.70.04713.83795980260.0230.0530.0472698.3
3.8-5.384.30.03916.42523358420.020.0440.0393092
5.38-37.95850.0413.71744034720.0190.0450.0430.798.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2eu9

2eu9


Resolution: 1.7→37.99 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1919 / WRfactor Rwork: 0.1527 / FOM work R set: 0.8556 / SU B: 4.266 / SU ML: 0.069 / SU R Cruickshank DPI: 0.0879 / SU Rfree: 0.0923 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 5204 5 %RANDOM
Rwork0.1565 ---
obs0.1584 98842 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.24 Å2 / Biso mean: 26.552 Å2 / Biso min: 8.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å2-0 Å2-0.84 Å2
2---0.53 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.7→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 195 929 7009
Biso mean--42.01 41.36 -
Num. residues----715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136393
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175866
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.6578612
X-RAY DIFFRACTIONr_angle_other_deg1.4411.58113642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68121.865370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.503151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5421545
X-RAY DIFFRACTIONr_chiral_restr0.1020.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021424
Refine LS restraints NCS

Ens-ID: 1 / Number: 12044 / 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: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 385 -
Rwork0.295 7353 -
all-7738 -
obs--96.4 %
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)
10.1057-0.01080.1660.1956-0.30241.27220.01980.0594-0.0407-0.01590.01340.01460.12080.1326-0.03330.03170.0352-0.0070.0594-0.02060.020712.728677.26185.0161
20.2520.011-0.05260.21770.03110.14480.0473-0.02680.00640.0457-0.0258-0.01050.04230.0091-0.02150.05770.00710.00470.04430.01230.01043.470582.354729.8344
31.8910.31491.47060.56111.23933.1069-0.2345-0.10290.29160.0419-0.08340.09240.0041-0.23230.31790.10320.0079-0.03490.0706-0.01320.0509-13.434120.38256.6812
40.23670.19860.0710.16890.09020.6489-0.0747-0.00720.0274-0.0668-0.00970.0297-0.1752-0.00060.08430.09230.0022-0.04080.0095-0.01550.04185.195126.69718.3281
50.08890.0481-0.14141.00380.48060.6350.0201-0.088-0.00590.0357-0.0108-0.0872-0.10620.1596-0.00920.0706-0.0209-0.03370.0907-0.00250.026219.2194124.584826.9137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 321
2X-RAY DIFFRACTION2A322 - 482
3X-RAY DIFFRACTION3B128 - 216
4X-RAY DIFFRACTION4B217 - 385
5X-RAY DIFFRACTION5B386 - 484

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