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- PDB-6z4z: Crystal structure of CLK1 in complex with macrocycle ODS2004070 -

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Basic information

Entry
Database: PDB / ID: 6z4z
TitleCrystal structure of CLK1 in complex with macrocycle ODS2004070
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / kinase / kinase inhibitor / clk1 / macrocycle / nanocyclic / 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
: / 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. ...: / 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 CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsChaikuad, A. / Benderitter, P. / Hoflack, J. / Denis, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of CLK1 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Dual specificity protein kinase CLK1
B: Dual specificity protein kinase CLK1
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,23811
Polymers118,7453
Non-polymers1,4938
Water7,530418
1
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2996
Polymers39,5821
Non-polymers7175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9222
Polymers39,5821
Non-polymers3401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0173
Polymers39,5821
Non-polymers4352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.290, 116.670, 91.291
Angle α, β, γ (deg.)90.000, 98.590, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-1 - 4811 - 336
21BB-1 - 4811 - 336
12AA-1 - 4821 - 337
22CC-1 - 4821 - 337
13BB-1 - 4811 - 336
23CC-1 - 4811 - 336

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 39581.512 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Plasmid: pLIC-SGC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: P49759, dual-specificity kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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.: 3 / Source method: obtained synthetically / Formula: C17H16N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 17.5% isopropanol, 5% glycerol, 0.1M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.07→30.9 Å / Num. obs: 70856 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.068 / Rrim(I) all: 0.15 / Net I/av σ(I): 3.2 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.07-2.184.40.7212103160.3760.8170.72199.9
2.18-2.314.40.5191.497490.2710.5880.51999.8
2.31-2.474.40.3761.991810.1950.4260.37699.8
2.47-2.674.40.2632.785400.1370.2980.26399.8
2.67-2.934.60.193.778820.0960.2130.1999.9
2.93-3.274.60.1374.771180.0690.1540.137100
3.27-3.784.60.1065.363080.0530.1190.106100
3.78-4.634.50.0955.853450.0480.1070.095100
4.63-6.554.50.0985.741270.050.110.098100
6.55-30.0894.40.0925.422900.0480.1040.09299

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6g33

6g33


Resolution: 2.07→30.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.95 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1932 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 3463 4.9 %RANDOM
Rwork0.1749 ---
obs0.1767 67366 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.13 Å2 / Biso mean: 27.847 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å2-0.11 Å2
2--1.66 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.07→30.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8274 0 107 418 8799
Biso mean--39.12 47.72 -
Num. residues----1013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198630
X-RAY DIFFRACTIONr_bond_other_d0.0060.028105
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.95111681
X-RAY DIFFRACTIONr_angle_other_deg1.068318671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71251022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37223.333420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.394151506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8951557
X-RAY DIFFRACTIONr_chiral_restr0.0880.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029892
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022073
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A21393
12B21393
21A21555
22C21555
31B21367
32C21367
LS refinement shellResolution: 2.07→2.124 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 247 -
Rwork0.288 4996 -
all-5243 -
obs--99.85 %
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)
13.80130.2396-1.17681.14440.29172.52650.1625-0.0511-0.3514-0.0558-0.14020.14610.1432-0.2487-0.02220.0828-0.0301-0.06740.1610.03450.090113.231659.542476.8442
22.05130.6690.20764.09170.19674.02650.05140.2838-0.4015-0.72950.0037-0.37070.22060.1371-0.05510.16440.05610.02520.2249-0.04590.182731.089958.219961.5861
34.2522-1.4862-0.31032.29580.53422.0277-0.0460.05210.0993-0.09590.02150.0444-0.05270.15650.02450.0214-0.0256-0.00310.0439-0.00080.006713.2428.568335.0226
42.978-1.14930.32123.97680.21754.7917-0.194-0.1040.59870.19660.10160.0542-0.74740.01480.09240.13620.0211-0.01260.1806-0.02430.2544-3.643745.331642.0116
53.9370.85480.27811.7724-0.15041.9740.0522-0.32310.21950.11190.0142-0.2259-0.08630.3372-0.06640.06040.04390.02820.22090.02050.115337.405221.830569.9088
62.0474-0.3529-0.49433.09320.5853.8528-0.0284-0.1013-0.30950.09530.09570.12130.6512-0.1599-0.06740.1128-0.0147-0.0170.22280.06650.06320.13463.724969.28
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 387
2X-RAY DIFFRACTION2A388 - 482
3X-RAY DIFFRACTION3B-1 - 336
4X-RAY DIFFRACTION4B337 - 484
5X-RAY DIFFRACTION5C-1 - 335
6X-RAY DIFFRACTION6C336 - 482

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