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- PDB-3nr9: Structure of human CDC2-like kinase 2 (CLK2) -

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Basic information

Entry
Database: PDB / ID: 3nr9
TitleStructure of human CDC2-like kinase 2 (CLK2)
ComponentsDual specificity protein kinase CLK2
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / PROTEIN KINASE / dual specificity protein kinase
Function / homology
Function and homology information


dual-specificity kinase / response to ionizing radiation / regulation of RNA splicing / negative regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / protein tyrosine kinase activity / protein autophosphorylation / nuclear body / nuclear speck / protein phosphorylation ...dual-specificity kinase / response to ionizing radiation / regulation of RNA splicing / negative regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / protein tyrosine kinase activity / protein autophosphorylation / nuclear body / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NR9 / Dual specificity protein kinase CLK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsChaikuad, A. / Savitsky, P. / Krojer, T. / Muniz, J.R.C. / Filippakopoulos, P. / Rellos, P. / Keates, T. / Fedorov, O. / Pike, A.C.W. / Eswaran, J. ...Chaikuad, A. / Savitsky, P. / Krojer, T. / Muniz, J.R.C. / Filippakopoulos, P. / Rellos, P. / Keates, T. / Fedorov, O. / Pike, A.C.W. / Eswaran, J. / Berridge, G. / Phillips, C. / Zhang, Y. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of human CDC2-like kinase 2 (CLK2)
Authors: Chaikuad, A. / Savitsky, P. / Krojer, T. / Muniz, J.R.C. / Filippakopoulos, P. / Rellos, P. / Keates, T. / Fedorov, O. / Pike, A.C.W. / Eswaran, J. / Berridge, G. / Phillips, C. / Zhang, Y. ...Authors: Chaikuad, A. / Savitsky, P. / Krojer, T. / Muniz, J.R.C. / Filippakopoulos, P. / Rellos, P. / Keates, T. / Fedorov, O. / Pike, A.C.W. / Eswaran, J. / Berridge, G. / Phillips, C. / Zhang, Y. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 CLK2
B: Dual specificity protein kinase CLK2
C: Dual specificity protein kinase CLK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,2196
Polymers130,1653
Non-polymers1,0543
Water1,13563
1
A: Dual specificity protein kinase CLK2
hetero molecules

A: Dual specificity protein kinase CLK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4794
Polymers86,7762
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area3130 Å2
ΔGint-1 kcal/mol
Surface area30090 Å2
MethodPISA
2
B: Dual specificity protein kinase CLK2
hetero molecules

C: Dual specificity protein kinase CLK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4794
Polymers86,7762
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3010 Å2
ΔGint-3 kcal/mol
Surface area30020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.678, 97.678, 223.029
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12A
22B
32C
13A
23B
14A
24C
15B
25A
35C
16A
26C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGGLYGLY2BB138 - 14910 - 21
211ARGARGGLYGLY2AA138 - 14910 - 21
112GLUGLUGLNGLN1AA213 - 22885 - 100
212GLUGLUGLNGLN1BB213 - 22885 - 100
312GLUGLUGLNGLN1CC213 - 22885 - 100
122ILEILEGLUGLU1AA241 - 304113 - 176
222ILEILEGLUGLU1BB241 - 304113 - 176
322ILEILEGLUGLU1CC241 - 304113 - 176
132VALVALMETMET1AA318 - 393190 - 265
232VALVALMETMET1BB318 - 393190 - 265
332VALVALMETMET1CC318 - 393190 - 265
142ARGARGPHEPHE1AA440 - 478312 - 350
242ARGARGPHEPHE1BB440 - 478312 - 350
342ARGARGPHEPHE1CC440 - 478312 - 350
113HISHISLEULEU1AA150 - 21222 - 84
213HISHISLEULEU1BB150 - 21222 - 84
123METMETCYSCYS1AA229 - 240101 - 112
223METMETCYSCYS1BB229 - 240101 - 112
114HISHISLEULEU4AA150 - 21222 - 84
214HISHISLEULEU4CC150 - 21222 - 84
124METMETCYSCYS4AA229 - 240101 - 112
224METMETCYSCYS4CC229 - 240101 - 112
115GLUGLUILEILE4BB394 - 400266 - 272
215GLUGLUILEILE4AA394 - 400266 - 272
315GLUGLUILEILE4CC394 - 400266 - 272
116PROPROLYSLYS1AA401 - 412273 - 284
216PROPROLYSLYS1CC401 - 412273 - 284
126TYRTYRARGARG4AA413 - 439285 - 311
226TYRTYRARGARG4CC413 - 439285 - 311

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Dual specificity protein kinase CLK2 / CDC-like kinase 2


Mass: 43388.180 Da / Num. of mol.: 3 / Fragment: UNP residue 135-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-lambda-PPase / References: UniProt: P49760, dual-specificity kinase
#2: Chemical ChemComp-NR9 / (5Z)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one


Mass: 351.445 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H13N3OS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9.3
Details: 25% MPD, 0.1M Bicine, pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2010 / Details: two K-B pairs of bimorph type mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.89→55.9 Å / Num. all: 28186 / Num. obs: 28133 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 65.9 Å2 / Rmerge(I) obs: 0.173 / Net I/σ(I): 8.5
Reflection shellResolution: 2.89→3.04 Å / Redundancy: 5 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 2 / Num. unique all: 4062 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0066refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EU9

2eu9


Resolution: 2.89→48.84 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 34.138 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25193 1416 5 %RANDOM
Rwork0.19399 ---
obs0.19686 26717 98.73 %-
all-28133 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.575 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å21.28 Å20 Å2
2--2.57 Å20 Å2
3----3.85 Å2
Refine analyzeLuzzati coordinate error obs: 0.379 Å
Refinement stepCycle: LAST / Resolution: 2.89→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8427 0 72 63 8562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0218721
X-RAY DIFFRACTIONr_bond_other_d0.0020.025903
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.94511812
X-RAY DIFFRACTIONr_angle_other_deg1.0123.00114185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84451031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15223.224456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.084151443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2451570
X-RAY DIFFRACTIONr_chiral_restr0.0750.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029772
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021921
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B71TIGHT POSITIONAL0.030.05
11B91MEDIUM POSITIONAL0.030.5
11B71TIGHT THERMAL5.080.5
11B91MEDIUM THERMAL6.262
21A2614TIGHT POSITIONAL0.050.05
22B2614TIGHT POSITIONAL0.040.05
23C2614TIGHT POSITIONAL0.040.05
21A2614TIGHT THERMAL3.290.5
22B2614TIGHT THERMAL3.780.5
23C2614TIGHT THERMAL3.340.5
31A1008TIGHT POSITIONAL0.050.05
31A1008TIGHT THERMAL3.250.5
41A1029MEDIUM POSITIONAL0.390.5
41A1029MEDIUM THERMAL2.362
51B99MEDIUM POSITIONAL0.670.5
52A99MEDIUM POSITIONAL0.380.5
53C99MEDIUM POSITIONAL0.370.5
51B99MEDIUM THERMAL2.362
52A99MEDIUM THERMAL2.172
53C99MEDIUM THERMAL1.392
61A176TIGHT POSITIONAL0.310.05
61A405MEDIUM POSITIONAL0.440.5
61A176TIGHT THERMAL2.480.5
61A405MEDIUM THERMAL2.572
LS refinement shellResolution: 2.89→2.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 108 -
Rwork0.313 1950 -
obs--98.52 %
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)
11.2318-0.52171.16962.5085-0.7532.01890.0506-0.1301-0.1457-0.06390.11340.18260.0414-0.1171-0.16390.16640.00940.0230.15950.02820.0380.78642.19386.8219
26.5836-0.0856-1.90344.4485-2.29334.2513-0.00920.17690.6973-0.40580.0120.0832-0.3346-0.4272-0.00280.24280.0892-0.00620.1451-0.02080.140279.607613.087-4.5685
31.7812-0.6001-1.24110.61670.35392.0754-0.01240.06580.10040.05250.07870.0721-0.1401-0.1817-0.06630.0820.0308-0.01260.10430.0410.044887.55250.9789-17.2417
44.8320.00191.61811.75680.23152.4274-0.01040.295-0.1561-0.22880.07330.1090.0385-0.2101-0.0630.1019-0.00750.00820.12890.00850.020191.0576-6.227-30.3727
521.20067.29510.67442.5481-0.10644.6958-0.10530.05460.224-0.0284-0.00780.14220.1939-0.43280.11320.38010.02350.08310.3684-0.0790.492837.863520.025633.2516
64.24230.0923-0.58224.9171-0.57493.33920.02920.12780.1745-0.1379-0.12010.5625-0.0478-0.69010.0910.28390.07530.02620.5742-0.09350.383527.989823.511522.6701
71.77730.8664-0.64383.2746-0.67312.81590.0141-0.0691-0.0007-0.1389-0.07920.20580.0725-0.37260.0650.21250.0382-0.07670.3065-0.03580.172542.190722.50534.2834
82.05880.36171.10613.28540.8793.5624-0.02120.2567-0.2908-0.414-0.08150.10520.3672-0.2530.10270.3687-0.024-0.01750.32660.00930.238945.874119.9757-6.9599
911.67546.20933.362916.4744-13.538619.4294-0.08711.4528-0.7463-0.3560.4597-0.90630.09380.5693-0.37260.3054-0.01360.35690.4453-0.00620.820949.4161-23.920859.3445
107.30463.0790.20614.094-0.43475.06080.1398-0.2505-0.17320.3287-0.1408-0.09620.140.12150.00110.30360.05450.02510.12890.0370.118370.6036-26.9656.8259
112.0303-0.53231.8115.64180.29652.22320.17830.2841-0.3838-0.2534-0.0542-0.32560.61110.3125-0.12410.57810.10880.14870.288-0.0030.383772.1468-34.129646.3024
121.68210.19070.28580.85590.01171.494-0.05740.0336-0.0707-0.04140.02630.02080.3182-0.08050.03110.23610.03280.01340.2084-0.00190.129559.6904-24.723331.4872
136.97012.87690.17131.5343-0.71492.0963-0.17150.3120.6936-0.03320.20730.4244-0.1932-0.5139-0.03580.32350.0608-0.12030.5443-0.09260.439340.5181-18.858724.1913
143.26782.2044-1.22038.4732-2.16864.0204-0.11240.269-0.0849-0.14170.0386-0.40660.3260.15530.07380.32580.0143-0.06740.2960.00960.120463.3566-23.985618.3582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A137 - 183
2X-RAY DIFFRACTION2A184 - 224
3X-RAY DIFFRACTION3A225 - 417
4X-RAY DIFFRACTION4A418 - 484
5X-RAY DIFFRACTION5B136 - 165
6X-RAY DIFFRACTION6B166 - 245
7X-RAY DIFFRACTION7B246 - 422
8X-RAY DIFFRACTION8B423 - 482
9X-RAY DIFFRACTION9C137 - 144
10X-RAY DIFFRACTION10C145 - 200
11X-RAY DIFFRACTION11C201 - 251
12X-RAY DIFFRACTION12C252 - 414
13X-RAY DIFFRACTION13C415 - 441
14X-RAY DIFFRACTION14C442 - 483

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