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- PDB-5yv9: Structure of CaMKK2 in complex with CKI-009 -

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Basic information

Entry
Database: PDB / ID: 5yv9
TitleStructure of CaMKK2 in complex with CKI-009
ComponentsCalcium/calmodulin-dependent protein kinase kinase 2
KeywordsTRANSFERASE / ATP-BINDING / KINASE / SERINE/THREONINE-PROTEIN KINASE / PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / calcium/calmodulin-dependent protein kinase activity / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / Activation of AMPK downstream of NMDARs / calcium-mediated signaling ...positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / calcium/calmodulin-dependent protein kinase activity / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / Activation of AMPK downstream of NMDARs / calcium-mediated signaling / cellular response to reactive oxygen species / MAPK cascade / protein tyrosine kinase activity / protein autophosphorylation / calmodulin binding / neuron projection / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / cytosol
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-91O / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsNiwa, H. / Handa, N. / Yokoyama, S.
CitationJournal: J.Mol.Graph.Model. / Year: 2020
Title: Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method.
Authors: Takaya, D. / Niwa, H. / Mikuni, J. / Nakamura, K. / Handa, N. / Tanaka, A. / Yokoyama, S. / Honma, T.
History
DepositionNov 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 10, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Nov 22, 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
Item: _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
A: Calcium/calmodulin-dependent protein kinase kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2935
Polymers33,7121
Non-polymers5814
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-11 kcal/mol
Surface area13080 Å2
Unit cell
Length a, b, c (Å)66.823, 78.017, 83.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase kinase 2 / CaMKK 2 / Calcium/calmodulin-dependent protein kinase kinase beta / CaMKK beta


Mass: 33711.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMKK2, CAMKKB, KIAA0787 / Plasmid: PX070406-05 / Production host: CELL-FREE SYNTHESIS (others)
References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-91O / 5-chloro-2-methoxy-4[(1Z)-3-(4-methoxyphenyl)-3-oxoprop-1-en-1-yl]aminobenzoic acid


Mass: 361.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16ClNO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Na cocodylate pH 6.5, 0.2M Na acetate, 20% PEG 8000, 0.03M Glycyl-glycyl-glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 15204 / % possible obs: 98.8 % / Redundancy: 7.4 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.102 / Rsym value: 0.095 / Net I/σ(I): 23.9
Reflection shellResolution: 2.53→2.57 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 757 / CC1/2: 0.675 / Rpim(I) all: 0.456 / Rrim(I) all: 1.237 / Rsym value: 1.149 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZV2

2zv2


Resolution: 2.53→36.882 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 24.66
RfactorNum. reflection% reflection
Rfree0.2218 764 5.03 %
Rwork0.1675 --
obs0.17 15167 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.53→36.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 38 79 2211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092176
X-RAY DIFFRACTIONf_angle_d0.9292941
X-RAY DIFFRACTIONf_dihedral_angle_d14.7191318
X-RAY DIFFRACTIONf_chiral_restr0.058324
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5157-2.60560.37911360.28572561X-RAY DIFFRACTION94
2.6056-2.70990.28181530.25882706X-RAY DIFFRACTION99
2.7099-2.83320.35071220.23012678X-RAY DIFFRACTION99
2.8332-2.98250.28071560.21392698X-RAY DIFFRACTION99
2.9825-3.16930.31591470.20072686X-RAY DIFFRACTION99
3.1693-3.41380.24691590.18952673X-RAY DIFFRACTION99
3.4138-3.75710.21891450.16322712X-RAY DIFFRACTION99
3.7571-4.30.17911450.13562730X-RAY DIFFRACTION100
4.3-5.41480.18211180.13282733X-RAY DIFFRACTION99
5.4148-36.88640.16491430.14232712X-RAY DIFFRACTION100
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)
17.02880.1121-0.02547.9239-1.77398.34290.01790.78250.1336-1.40310.0942-0.45080.63370.4799-0.12650.6221-0.01260.03880.5929-0.04570.38413.1996-9.1475-34.6051
22.46410.16660.26894.3101-1.49855.07040.04780.09570.0616-0.38550.10120.00560.0270.3057-0.13960.2943-0.0229-0.00070.3599-0.05320.42960.4914-14.8807-17.6817
36.8375-1.5889-0.22033.9632-0.25762.94460.024-0.48310.42960.45780.0906-0.1927-0.18140.5327-0.14350.3945-0.0752-0.01370.5288-0.08060.32324.5105-15.3592-1.0471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 243 )
2X-RAY DIFFRACTION2chain 'A' and (resid 244 through 386 )
3X-RAY DIFFRACTION3chain 'A' and (resid 387 through 448 )

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