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- PDB-6g33: Crystal structure of CLK1 in complex with 5-iodotubercidin -

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Basic information

Entry
Database: PDB / ID: 6g33
TitleCrystal structure of CLK1 in complex with 5-iodotubercidin
Components(Dual specificity protein kinase ...) x 2
KeywordsTRANSFERASE / kinase / inhibitors / slow off-rate / kinetics / 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
Chem-5ID / IODIDE ION / PHOSPHATE ION / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHeroven, C. / Chaikuad, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Halogen-Aromatic pi Interactions Modulate Inhibitor Residence Times.
Authors: Heroven, C. / Georgi, V. / Ganotra, G.K. / Brennan, P. / Wolfreys, F. / Wade, R.C. / Fernandez-Montalvan, A.E. / Chaikuad, A. / Knapp, S.
History
DepositionMar 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)120,55710
Polymers118,9043
Non-polymers1,6527
Water6,143341
1
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3554
Polymers39,7411
Non-polymers6143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1013
Polymers39,5821
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1013
Polymers39,5821
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.181, 116.191, 90.980
Angle α, β, γ (deg.)90.00, 98.99, 90.00
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: _ / Auth seq-ID: -1 - 482 / Label seq-ID: 1 - 337

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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Dual specificity protein kinase ... , 2 types, 3 molecules ABC

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


Mass: 39741.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: P49759, dual-specificity kinase
#2: Protein Dual specificity protein kinase CLK1 / CDC-like kinase 1


Mass: 39581.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: P49759, dual-specificity kinase

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Non-polymers , 4 types, 348 molecules

#3: Chemical ChemComp-5ID / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / 5-IODOTUBERCIDIN


Mass: 392.150 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H13IN4O4
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% 1,2-propanediol, 5% glycerol and 0.1 M NaKPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0282 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0282 Å / Relative weight: 1
ReflectionResolution: 2.05→29.34 Å / Num. obs: 72225 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.2
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 10553 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vag

2vag


Resolution: 2.05→89.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.983 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21829 3576 5 %RANDOM
Rwork0.18824 ---
obs0.18971 68534 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å20.33 Å2
2---0.6 Å2-0 Å2
3---0.72 Å2
Refinement stepCycle: 1 / Resolution: 2.05→89.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8205 0 68 341 8614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198605
X-RAY DIFFRACTIONr_bond_other_d0.0080.027987
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.94511677
X-RAY DIFFRACTIONr_angle_other_deg1.277318411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07451024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28123.565418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.017151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1671552
X-RAY DIFFRACTIONr_chiral_restr0.0950.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029928
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022058
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5752.5174063
X-RAY DIFFRACTIONr_mcbond_other1.5752.5174056
X-RAY DIFFRACTIONr_mcangle_it2.573.7665070
X-RAY DIFFRACTIONr_mcangle_other2.573.7665071
X-RAY DIFFRACTIONr_scbond_it1.9743.7454542
X-RAY DIFFRACTIONr_scbond_other1.9713.7424538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2396594
X-RAY DIFFRACTIONr_long_range_B_refined6.32520.86210000
X-RAY DIFFRACTIONr_long_range_B_other6.32520.86410001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded29.31656
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A410900.08
12B410900.08
21A405860.09
22C405860.09
31B411240.08
32C411240.08
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 267 -
Rwork0.292 5018 -
obs--99.55 %
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)
11.6591-0.7459-0.22350.84850.32680.789-0.04940-0.0115-0.01850.04920.062-0.01150.0690.00020.0061-0.0238-0.00080.31440.0110.160933.594544.326480.5913
21.0604-0.93260.01831.76370.45771.8146-0.1077-0.13050.14360.06730.06190.0839-0.3223-0.13770.04580.07220.0239-0.01560.3139-0.0150.226816.221460.395886.7144
31.1488-0.2191-0.21040.5459-0.2711.29430.22590.183-0.1263-0.0626-0.14770.05420.03770.2573-0.07820.05070.0697-0.04360.472-0.05710.153352.535816.844454.584
40.7572-0.3989-0.12921.8347-0.00980.72740.043-0.0591-0.19530.30890.02540.1120.0306-0.0193-0.06840.0754-0.0237-0.02290.28850.02380.199635.550414.950972.472
52.76530.18190.03190.3785-0.02411.76390.0553-0.17080.245-0.05750.00450.00120.00920.1608-0.05980.020.02660.04220.34740.0250.199857.8435.7259113.5047
61.1098-0.2426-0.16020.82850.41151.14840.0305-0.1253-0.0759-0.0360.06330.10660.2594-0.1274-0.09380.0954-0.0065-0.02180.35670.06170.168439.812118.4201114.3833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 346
2X-RAY DIFFRACTION2A347 - 482
3X-RAY DIFFRACTION3B-1 - 336
4X-RAY DIFFRACTION4B337 - 482
5X-RAY DIFFRACTION5C-1 - 346
6X-RAY DIFFRACTION6C347 - 482

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