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- PDB-5yv8: Structure of CaMKK2 in complex with CKI-002 -

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Basic information

Entry
Database: PDB / ID: 5yv8
TitleStructure of CaMKK2 in complex with CKI-002
ComponentsCalcium/calmodulin-dependent protein kinase kinase 2
KeywordsTRANSFERASE / ATP-BINDING / KINASE / SERINE/THREONINE-PROTEIN KINASE / PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


regulation of protein kinase activity / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calcium/calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / Activation of AMPK downstream of NMDARs / cellular response to reactive oxygen species ...regulation of protein kinase activity / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calcium/calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / Activation of AMPK downstream of NMDARs / cellular response to reactive oxygen species / calcium-mediated signaling / MAPK cascade / positive regulation of protein phosphorylation / protein autophosphorylation / protein tyrosine kinase activity / calmodulin binding / neuron projection / 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-91L / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.927 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)34,3997
Polymers33,7121
Non-polymers6876
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-12 kcal/mol
Surface area13030 Å2
Unit cell
Length a, b, c (Å)66.493, 76.969, 83.895
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-91L / 1-amino-4-hydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid


Mass: 283.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H9NO5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / 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.: 277 / Source method: isolated from a natural source / Formula: H2O
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: 3.19 Å3/Da / Density % sol: 61.49 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium cacodylate (pH 6.0), 0.2M Sodium acetate, 22% 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: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 33185 / % possible obs: 100 % / Redundancy: 7.4 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.097 / Rsym value: 0.09 / Net I/σ(I): 22.2
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1621 / CC1/2: 0.769 / Rpim(I) all: 0.398 / Rrim(I) all: 1.082 / Rsym value: 1.005 / % possible all: 100

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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: 1.927→32.22 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 20.62 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2126 3192 5.09 %
Rwork0.1637 --
obs0.1661 33185 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.927→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 46 277 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082185
X-RAY DIFFRACTIONf_angle_d0.8412953
X-RAY DIFFRACTIONf_dihedral_angle_d14.5031318
X-RAY DIFFRACTIONf_chiral_restr0.061324
X-RAY DIFFRACTIONf_plane_restr0.006373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9272-1.9560.3491220.29212517X-RAY DIFFRACTION97
1.956-1.98660.29311300.2672575X-RAY DIFFRACTION100
1.9866-2.01910.31631730.2512572X-RAY DIFFRACTION100
2.0191-2.05390.23951480.22612556X-RAY DIFFRACTION100
2.0539-2.09130.22641350.21532616X-RAY DIFFRACTION100
2.0913-2.13150.25921550.19862585X-RAY DIFFRACTION100
2.1315-2.1750.24831360.19062565X-RAY DIFFRACTION100
2.175-2.22230.26811270.19982606X-RAY DIFFRACTION100
2.2223-2.2740.21891590.18352609X-RAY DIFFRACTION100
2.274-2.33080.23381480.17092562X-RAY DIFFRACTION100
2.3308-2.39380.19551150.16982625X-RAY DIFFRACTION100
2.3938-2.46420.21651350.16752577X-RAY DIFFRACTION100
2.4642-2.54370.21691440.16342616X-RAY DIFFRACTION100
2.5437-2.63460.21521340.15752571X-RAY DIFFRACTION100
2.6346-2.740.221510.16182596X-RAY DIFFRACTION100
2.74-2.86470.24661120.17022596X-RAY DIFFRACTION100
2.8647-3.01560.19391540.15892575X-RAY DIFFRACTION100
3.0156-3.20440.21161360.15972601X-RAY DIFFRACTION100
3.2044-3.45150.23451460.16082575X-RAY DIFFRACTION100
3.4515-3.79840.17451360.13692601X-RAY DIFFRACTION100
3.7984-4.34690.1781430.12812573X-RAY DIFFRACTION100
4.3469-5.47220.16751140.13722636X-RAY DIFFRACTION100
5.4722-32.22420.21161390.16112581X-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)
13.5098-0.7510.02382.8782-0.20182.037-0.1105-0.5574-0.23540.910.1510.30570.5249-0.3054-0.05110.5757-0.06330.0110.34890.0480.2761-1.5657-10.529534.6161
21.16770.08630.24922.84410.77911.58680.0454-0.04250.05230.20960.0112-0.0305-0.0484-0.0813-0.05840.13590.0169-0.01020.1680.02120.1483-0.7388-14.818315.2674
34.58560.1429-0.36261.1450.33141.32350.08270.29230.3253-0.2108-0.01660.0787-0.1361-0.1656-0.07440.21270.0202-0.00750.25570.05080.1619-4.5378-14.93851.0986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 262 )
2X-RAY DIFFRACTION2chain 'A' and (resid 263 through 386 )
3X-RAY DIFFRACTION3chain 'A' and (resid 387 through 448 )

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