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- PDB-6t29: Crystal structure of human calmodulin-dependent protein kinase 1D... -

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Basic information

Entry
Database: PDB / ID: 6t29
TitleCrystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 18 (CS587)
ComponentsCalcium/calmodulin-dependent protein kinase type 1D
KeywordsTRANSFERASE / Inhibitor / Complex / Kinase
Function / homology
Function and homology information


regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / positive regulation of neutrophil chemotaxis / calmodulin-dependent protein kinase activity / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development / nervous system development ...regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / positive regulation of neutrophil chemotaxis / calmodulin-dependent protein kinase activity / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development / nervous system development / calmodulin binding / inflammatory response / positive regulation of apoptotic process / phosphorylation / protein serine kinase activity / negative regulation of apoptotic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Chem-M8Z / Calcium/calmodulin-dependent protein kinase type 1D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.484 Å
AuthorsKraemer, A. / Sorrell, F. / Butterworth, S. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust202708 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Highly Selective Inhibitors of Calmodulin-Dependent Kinases That Restore Insulin Sensitivity in the Diet-Induced Obesityin VivoMouse Model.
Authors: Fromont, C. / Atzori, A. / Kaur, D. / Hashmi, L. / Greco, G. / Cabanillas, A. / Nguyen, H.V. / Jones, D.H. / Garzon, M. / Varela, A. / Stevenson, B. / Iacobini, G.P. / Lenoir, M. / Rajesh, S. ...Authors: Fromont, C. / Atzori, A. / Kaur, D. / Hashmi, L. / Greco, G. / Cabanillas, A. / Nguyen, H.V. / Jones, D.H. / Garzon, M. / Varela, A. / Stevenson, B. / Iacobini, G.P. / Lenoir, M. / Rajesh, S. / Box, C. / Kumar, J. / Grant, P. / Novitskaya, V. / Morgan, J. / Sorrell, F.J. / Redondo, C. / Kramer, A. / Harris, C.J. / Leighton, B. / Vickers, S.P. / Cheetham, S.C. / Kenyon, C. / Grabowska, A.M. / Overduin, M. / Berditchevski, F. / Weston, C.J. / Knapp, S. / Fischer, P.M. / Butterworth, S.
History
DepositionOct 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Calcium/calmodulin-dependent protein kinase type 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,11411
Polymers42,9731
Non-polymers1,14110
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-42 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.820, 45.640, 108.754
Angle α, β, γ (deg.)90.000, 104.183, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11AAA-658-

HOH

21AAA-692-

HOH

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase type 1D / CaM kinase I delta / CaMKID / CaMKI-like protein kinase / CKLiK


Mass: 42972.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK1D, CAMKID / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IU85, Ca2+/calmodulin-dependent protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-M8Z / 2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3,5-bis(2-cyanopropan-2-yl)phenyl]amino]pyrimidine-5-carboxamide


Mass: 446.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30N8O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 0,1M NaCit, pH 5.9 2,05M AmmSO4 0,1M Na/K tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.48→55.45 Å / Num. obs: 44955 / % possible obs: 98.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 14.8
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 14295 / CC1/2: 0.883 / Rpim(I) all: 0.155 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jc6

2jc6


Resolution: 1.484→55.448 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.14 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1747 2291 5.096 %
Rwork0.1355 --
all0.137 --
obs-44954 98.465 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.727 Å2-0 Å2-0.17 Å2
2---0.188 Å20 Å2
3----0.402 Å2
Refinement stepCycle: LAST / Resolution: 1.484→55.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 73 197 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132324
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172120
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.6443148
X-RAY DIFFRACTIONr_angle_other_deg1.4161.5954918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00623.839112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75115389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.923158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02471
X-RAY DIFFRACTIONr_nbd_refined0.2150.2417
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.21916
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21129
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2148
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.214
X-RAY DIFFRACTIONr_nbd_other0.1630.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.220
X-RAY DIFFRACTIONr_mcbond_it1.7141.6681114
X-RAY DIFFRACTIONr_mcbond_other1.7131.6691115
X-RAY DIFFRACTIONr_mcangle_it2.3242.5121396
X-RAY DIFFRACTIONr_mcangle_other2.3232.5131397
X-RAY DIFFRACTIONr_scbond_it2.2311.9541210
X-RAY DIFFRACTIONr_scbond_other2.231.9541211
X-RAY DIFFRACTIONr_scangle_it2.8152.8131752
X-RAY DIFFRACTIONr_scangle_other2.8152.8131753
X-RAY DIFFRACTIONr_lrange_it3.53520.432595
X-RAY DIFFRACTIONr_lrange_other3.53520.4272595
X-RAY DIFFRACTIONr_rigid_bond_restr1.434444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.484-1.5230.2051610.1573131X-RAY DIFFRACTION98.3274
1.523-1.5640.1841700.1443044X-RAY DIFFRACTION98.4078
1.564-1.610.1951760.1342945X-RAY DIFFRACTION98.3922
1.61-1.6590.1731580.1152870X-RAY DIFFRACTION97.583
1.659-1.7130.1531460.1072771X-RAY DIFFRACTION98.0834
1.713-1.7730.1581310.1042730X-RAY DIFFRACTION98.7233
1.773-1.840.1731460.1042629X-RAY DIFFRACTION98.7544
1.84-1.9150.1561170.1062549X-RAY DIFFRACTION98.7042
1.915-20.1711420.1092375X-RAY DIFFRACTION97.4826
2-2.0980.1541200.1152316X-RAY DIFFRACTION98.464
2.098-2.2110.161290.1222196X-RAY DIFFRACTION98.4752
2.211-2.3450.151160.1142099X-RAY DIFFRACTION99.4165
2.345-2.5070.146870.1141988X-RAY DIFFRACTION98.3412
2.507-2.7070.167960.1311821X-RAY DIFFRACTION98.0563
2.707-2.9650.183860.1411719X-RAY DIFFRACTION99.6687
2.965-3.3140.157780.1481552X-RAY DIFFRACTION99.4509
3.314-3.8240.213620.1471356X-RAY DIFFRACTION97.3901
3.824-4.6780.153780.1491147X-RAY DIFFRACTION99.6745
4.678-6.5920.23560.218912X-RAY DIFFRACTION98.9775

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