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- PDB-4yuq: CDPK1 from Eimeria tenella in complex with inhibitor UW1354 -

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Basic information

Entry
Database: PDB / ID: 4yuq
TitleCDPK1 from Eimeria tenella in complex with inhibitor UW1354
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-KS1 / Calmodulin-like domain protein kinase
Similarity search - Component
Biological speciesEimeria tenella (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 19, 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 ...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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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: Calmodulin-like domain protein kinase
B: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,29612
Polymers111,3372
Non-polymers95910
Water0
1
A: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1486
Polymers55,6691
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1486
Polymers55,6691
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.701, 94.253, 87.395
Angle α, β, γ (deg.)90.000, 93.060, 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 / Mutation: A410D
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-KS1 / 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 319.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17N7
Sequence detailsAUTHOR STATED THAT THE UNP REFERENCE Q3HNM4 IS INCORRECT AT RESIDUE 410. THE RESIDUE IDENTITY OF ...AUTHOR STATED THAT THE UNP REFERENCE Q3HNM4 IS INCORRECT AT RESIDUE 410. THE RESIDUE IDENTITY OF 410 SHOULD BE ASP INSTEAD OF ALA BECAUSE THIS RESIDUE IS IN BINDING TO CALCIUM AND CONSERVED ACROSS THE LARGER FAMILY OF CDPKS.

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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: 2.54 Å3/Da / Density % sol: 51.53 %
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 ??M EtCDPK1, 350 uM UW1354; crystallization buffer: 100 mM HEPES pH 7.0, 25% PEG 3350, 1.75% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 26844 / % possible obs: 96.6 % / Redundancy: 3 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.126 / Rrim(I) all: 0.206 / Χ2: 0.806 / Net I/av σ(I): 5.69 / Net I/σ(I): 2.8 / Num. measured all: 81339
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.8-2.852.311840.4230.7450.43584.4
2.85-2.92.712660.4430.6970.456950.982
2.9-2.962.813570.4570.680.46397.40.975
2.96-3.02313610.630.5890.50198.20.876
3.02-3.083.113600.5990.5040.49198.80.7680.923
3.08-3.153.213850.7080.4370.53698.30.6730.805
3.15-3.233.113300.80.3680.57498.20.5650.677
3.23-3.323.213560.8360.3010.55798.40.4610.552
3.32-3.423.113680.8770.2670.6498.10.4050.487
3.42-3.533.113480.8790.2320.69797.50.3460.419
3.53-3.652.813010.920.1850.71493.50.2640.325
3.65-3.8313450.9470.1470.86296.10.2180.264
3.8-3.973.313390.9520.1260.89298.40.1930.231
3.97-4.183.313800.9530.1131.00798.20.1720.207
4.18-4.443.213520.9670.0881.03698.50.1340.161
4.44-4.793.213730.9690.0831.12698.10.1230.149
4.79-5.27313410.960.0891.03695.60.130.158
5.27-6.03313240.9520.0961.03295.40.140.171
6.03-7.583.213970.9660.0791.02898.30.1210.145
7.58-40313770.9790.0591.71795.60.0850.104

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ysj

4ysj


Resolution: 2.8→40 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.2536 / WRfactor Rwork: 0.2189 / FOM work R set: 0.6832 / SU B: 59.029 / SU ML: 0.484 / SU R Cruickshank DPI: 0.38 / SU Rfree: 0.4248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1314 4.9 %RANDOM
Rwork0.2403 ---
obs0.242 25349 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.72 Å2 / Biso mean: 67.338 Å2 / Biso min: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å2-0.83 Å2
2--3.08 Å20 Å2
3----1.02 Å2
Refinement stepCycle: final / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7347 0 56 0 7403
Biso mean--52.72 --
Num. residues----924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197575
X-RAY DIFFRACTIONr_bond_other_d0.0030.027249
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.96810134
X-RAY DIFFRACTIONr_angle_other_deg0.883316706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37724.755347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.111151405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4261540
X-RAY DIFFRACTIONr_chiral_restr0.0710.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028622
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021666
X-RAY DIFFRACTIONr_mcbond_it1.4883.0723699
X-RAY DIFFRACTIONr_mcbond_other1.4873.0723699
X-RAY DIFFRACTIONr_mcangle_it2.544.6024602
Refine LS restraints NCS

Ens-ID: 1 / Number: 29519 / 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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 86 -
Rwork0.37 1743 -
all-1829 -
obs--89.09 %
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)
17.25921.39553.89192.0581.04972.5993-0.14670.23-0.1649-0.06-0.12520.01590.10.19970.27180.5359-0.024-0.08760.18240.05990.40143.707-2.731-8.029
24.4573.3838-0.78886.54660.54894.8489-0.3977-0.0579-0.52450.05080.5005-0.23430.1325-0.038-0.10280.35770.0085-0.17450.22150.00170.32285.409-3.779-4.405
33.26531.21260.02462.3366-0.48891.0159-0.05660.013-0.0612-0.00540.173-0.054-0.0510.1492-0.11650.35680.0142-0.26610.059-0.04820.2307-9.481-12.417-1.782
44.4925-1.8721-0.43943.3144-0.37822.2924-0.0343-0.2685-0.560.28010.20760.42550.0736-0.2529-0.17340.27260.0131-0.18470.07580.03380.2762-21.536-21.9946.53
55.59652.3057-0.49684.2226-0.29830.42650.077-0.21690.31860.0680.0750.416-0.1914-0.3098-0.1520.54170.1073-0.23160.32090.11360.2781-20.7494.25-14.422
62.62473.16460.13013.84020.03622.49920.07870.13310.58120.00450.17430.7825-0.0495-0.7531-0.2530.59610.0345-0.34750.34410.05620.4165-27.3981.957-20.235
74.98710.9532-2.08623.91640.91415.56820.15110.34520.4334-0.6842-0.024-0.2487-0.59430.4808-0.12710.6536-0.0763-0.24230.30280.01970.3057-2.2848.006-23.988
81.2061-1.6802-1.8639.54246.18828.0157-0.19220.93190.4547-0.0792-0.15510.0661-0.2912-0.8450.34730.9541-0.0625-0.13911.02440.34210.5732-3.67215.494-30.344
91.1210.12011.26942.14830.85119.65780.0140.3910.1756-0.195-0.0953-0.105-0.21530.32430.08130.4596-0.0071-0.20970.19180.03720.3465-23.37-41.812-45.197
102.2008-0.7226-1.45683.06810.79943.87970.06670.3133-0.0694-0.09210.13890.0389-0.2045-0.2546-0.20560.4939-0.0528-0.32280.09730.03970.2554-31.451-38.26-38.025
113.00760.2006-0.03275.72610.60282.86390.10750.11930.02680.0857-0.04260.0375-0.3538-0.0747-0.06480.4105-0.0392-0.22190.01420.03580.1522-35.11-26.788-32.181
123.1532-1.2309-0.62652.96111.05383.9116-0.3456-0.2623-0.19550.68050.43760.6195-0.6835-0.6116-0.0920.86280.1681-0.10690.33620.18020.4945-45.798-21.809-24.437
132.22990.55650.1215.54230.56714.9332-0.2607-0.0808-0.45270.27960.13530.21220.1619-0.13430.12540.38220.001-0.18960.01240.03380.3327-24.061-50.253-22.253
149.3854-0.23670.26891.92182.21162.6127-0.2159-1.13510.01880.44280.04680.080.36450.02710.16910.6154-0.0974-0.2790.2673-0.00130.2322-23.033-46.635-6.713
154.9220.214-0.61838.0513-0.25814.03650.16110.1837-0.54030.1683-0.0244-0.39150.0892-0.0906-0.13660.2508-0.021-0.17940.0737-0.02150.1871-19.364-50.266-24.843
168.6662-0.4313-1.11523.24551.90132.49570.0149-0.0211-0.672-0.0205-0.0836-0.64140.3980.38090.06870.45310.0088-0.07760.46590.01130.5766-4.925-54.395-34.39
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 42
2X-RAY DIFFRACTION2A43 - 76
3X-RAY DIFFRACTION3A77 - 204
4X-RAY DIFFRACTION4A205 - 289
5X-RAY DIFFRACTION5A293 - 364
6X-RAY DIFFRACTION5A501
7X-RAY DIFFRACTION6A365 - 407
8X-RAY DIFFRACTION6A502
9X-RAY DIFFRACTION7A408 - 456
10X-RAY DIFFRACTION7A503
11X-RAY DIFFRACTION8A457 - 481
12X-RAY DIFFRACTION8A504
13X-RAY DIFFRACTION9B8 - 43
14X-RAY DIFFRACTION10B44 - 141
15X-RAY DIFFRACTION11B142 - 224
16X-RAY DIFFRACTION12B225 - 289
17X-RAY DIFFRACTION13B293 - 350
18X-RAY DIFFRACTION13B501
19X-RAY DIFFRACTION14B351 - 390
20X-RAY DIFFRACTION15B391 - 418
21X-RAY DIFFRACTION15B502
22X-RAY DIFFRACTION16B419 - 481
23X-RAY DIFFRACTION16B503
24X-RAY DIFFRACTION16B504

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