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- PDB-4yzb: CDPK1 from Eimeria tenella in complex with inhibitor UW1521 -

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Basic information

Entry
Database: PDB / ID: 4yzb
TitleCDPK1 from Eimeria tenella in complex with inhibitor UW1521
ComponentsCalmodulin-like domain protein kinase
KeywordsTransferase/Transferase Inhibitor / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / bumped kinase inhibitor / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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-BK8 / Calmodulin-like domain protein kinase
Similarity search - Component
Biological speciesEimeria tenella (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsMerritt, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089441 United States
CitationJournal: to be published
Title: CDPK is a druggable target in the apicomplexan parasite Eimeria
Authors: Ojo, K.K. / Vidadala, R. / Maly, D.J. / Van Voorhis, W.C. / Merritt, E.A.
History
DepositionMar 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-like domain protein kinase
B: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,46112
Polymers111,3372
Non-polymers1,12410
Water0
1
A: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2306
Polymers55,6691
Non-polymers5625
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2306
Polymers55,6691
Non-polymers5625
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.259, 97.950, 89.930
Angle α, β, γ (deg.)90.000, 94.560, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 8 - 480 / Label seq-ID: 12 - 484

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

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Components

#1: Protein Calmodulin-like domain protein kinase


Mass: 55668.504 Da / Num. of mol.: 2 / Fragment: full length
Source method: isolated from a genetically manipulated source
Details: cleaved N-terminal His-tag / Source: (gene. exp.) Eimeria tenella (eukaryote) / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3HNM4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BK8 / 4-(6-ethoxynaphthalen-2-yl)-6-(piperazin-1-ylmethyl)-2H-indazol-3-amine


Mass: 401.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N5O

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein buffer: 25 mM HEPES pH 7.0, 5% glycerol, 500 mM NaCl, 2 mM DTT, 175 uM EtCDPK1, 10 mM MgATP, 700 uM 1521; crystallization buffer: 100 mM BIS/TRIS pH 6.25 22% PEG 3350, 3.5% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.9→97.95 Å / Num. obs: 26054 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 52.5 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.322 / Rpim(I) all: 0.131 / Net I/σ(I): 4.8 / Num. measured all: 180788 / Scaling rejects: 322
Reflection shell

Diffraction-ID: 1 / Redundancy: 7.1 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.9-3.082.2370.92994041980.3220.89299.7
8.7-97.950.08116.3728610250.9950.03299.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
Aimless0.3.11data scaling
PHASERphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YSJ

4ysj


Resolution: 2.9→89.65 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.2576 / WRfactor Rwork: 0.2178 / FOM work R set: 0.6702 / SU ML: 0.527 / SU R Cruickshank DPI: 0.4237 / SU Rfree: 0.4778 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 1254 5 %RANDOM
Rwork0.2421 ---
obs0.2443 23745 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 185.65 Å2 / Biso mean: 78.63 Å2 / Biso min: 41.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å2-0 Å20.65 Å2
2--1.46 Å20 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 2.9→89.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7407 0 68 0 7475
Biso mean--66.01 --
Num. residues----930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197647
X-RAY DIFFRACTIONr_bond_other_d0.0040.027324
X-RAY DIFFRACTIONr_angle_refined_deg1.611.96810229
X-RAY DIFFRACTIONr_angle_other_deg0.953316875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69624.731353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.586151418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6511542
X-RAY DIFFRACTIONr_chiral_restr0.0810.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028740
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021686
X-RAY DIFFRACTIONr_mcbond_it1.6182.593721
X-RAY DIFFRACTIONr_mcbond_other1.6182.5913722
X-RAY DIFFRACTIONr_mcangle_it2.7483.8834634
Refine LS restraints NCS

Ens-ID: 1 / Number: 29577 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 92 -
Rwork0.363 1849 -
all-1941 -
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)
19.28322.7313.3783.340.6462.1234-0.09190.4093-0.0116-0.1728-0.0017-0.1747-0.08420.57320.09360.5217-0.002-0.16010.2448-0.06290.47984.969-7.041-7.987
23.40492.5055-0.46983.3125-1.02990.75650.0069-0.0261-0.0965-0.0170.0264-0.22120.03750.0765-0.03330.60470.0386-0.39670.0281-0.04310.4135-4.524-13.337-2.683
34.628-0.71410.15245.176-0.70563.30560.0088-0.0206-0.13420.04760.13110.25160.1532-0.2472-0.13990.4785-0.0006-0.3510.01990.00690.3689-17.29-26.3793.616
49.95960.2862.52965.4404-0.2371.53990.101-0.42380.67940.409-0.00580.6406-0.3363-0.8092-0.09520.81110.199-0.2830.64610.12170.5589-16.8372.362-14.443
59.9742.73-0.72363.65871.01035.41660.0008-0.07860.2968-0.36060.68161.0643-0.0623-1.1995-0.68250.6708-0.0002-0.41390.81510.41910.7507-28.563-4.56-19.101
65.52372.5427-3.04377.2777-1.38875.92330.24840.8520.858-1.06040.1754-0.5238-1.13280.0201-0.42380.99130.0264-0.23120.32070.07380.6522-2.8095.352-25.154
70.4843-0.43510.08173.99171.48069.1032-0.00710.407-0.0607-0.34560.1199-0.054-0.15650.1984-0.11280.5948-0.0647-0.21360.4121-0.02640.4081-22.743-50.957-47.524
83.3026-3.1712-0.62325.10812.75213.8579-0.2989-0.0356-0.39320.18770.40710.5611-0.04120.079-0.10820.72020.0159-0.40290.15660.150.5613-31.099-42.568-38.436
95.7085-1.2754-0.92286-1.17525.0958-0.6293-0.6938-0.16110.75130.6430.5741-0.2765-0.0986-0.01370.83480.2261-0.23010.18810.15790.5684-40.72-27.577-30.054
100.7727-0.4698-2.28596.5985-0.54278.3444-0.19270.1051-0.25060.2221-0.23570.51230.2256-0.63970.42840.4969-0.0102-0.24440.23460.07660.58-23.655-58.094-23.332
115.2983-0.9571-1.88913.11030.56089.6566-0.1811-0.6797-0.1050.41280.19120.1753-0.1429-0.1745-0.01010.50020.0222-0.32240.10990.03130.4108-22.285-53.638-14.666
1210.08671.7563-0.03946.9491-1.81784.3332-0.0151-0.321-1.0188-0.4212-0.3363-1.24390.51051.01990.35130.58480.0823-0.20170.3364-0.06190.7827-4.929-61.484-34.596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 41
2X-RAY DIFFRACTION2A42 - 161
3X-RAY DIFFRACTION3A162 - 294
4X-RAY DIFFRACTION4A295 - 343
5X-RAY DIFFRACTION5A344 - 401
6X-RAY DIFFRACTION5A501
7X-RAY DIFFRACTION5A502
8X-RAY DIFFRACTION6A402 - 480
9X-RAY DIFFRACTION6A503
10X-RAY DIFFRACTION6A504
11X-RAY DIFFRACTION7B8 - 51
12X-RAY DIFFRACTION8B52 - 171
13X-RAY DIFFRACTION9B172 - 287
14X-RAY DIFFRACTION10B294 - 344
15X-RAY DIFFRACTION11B345 - 417
16X-RAY DIFFRACTION11B501
17X-RAY DIFFRACTION11B502
18X-RAY DIFFRACTION12B418 - 480
19X-RAY DIFFRACTION12B503
20X-RAY DIFFRACTION12B504

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