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- PDB-6bqq: Crystal Structure of the Human CAMKK2B in complex with BI2526 -

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Basic information

Entry
Database: PDB / ID: 6bqq
TitleCrystal Structure of the Human CAMKK2B in complex with BI2526
ComponentsCalcium/calmodulin-dependent protein kinase kinase 2
KeywordsTRANSFERASE / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase 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 / protein tyrosine kinase activity / protein autophosphorylation / positive regulation of protein phosphorylation / 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
ACETATE ION / Chem-R78 / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCounago, R.M. / de Souza, G.P. / dos Reis, C.V. / Ramos, P.Z. / Drewry, D. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of the Human CAMKK2B in complex with BI2526
Authors: Counago, R.M. / de Souza, G.P. / dos Reis, C.V. / Drewry, D. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. / Structural Genomics Consortium (SGC)
History
DepositionNov 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent protein kinase kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8265
Polymers33,1271
Non-polymers6994
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.532, 73.532, 119.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 33127.250 Da / Num. of mol.: 1 / Fragment: residues 161-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMKK2, CAMKKB, KIAA0787 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H39N7O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 3350; 0.21 M Ammonium Sulphate; 0.1M CHC buffer pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→19.88 Å / Num. obs: 31086 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Rrim(I) all: 0.103 / Net I/σ(I): 15.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1798 / CC1/2: 0.786 / Rpim(I) all: 0.482 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UYJ

5uyj


Resolution: 1.8→19.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.882 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22768 1539 5 %RANDOM
Rwork0.19064 ---
obs0.19245 29482 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 50 180 2344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192211
X-RAY DIFFRACTIONr_bond_other_d0.0020.022059
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9752996
X-RAY DIFFRACTIONr_angle_other_deg0.9472.9734782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7912594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7815373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.237156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212416
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02408
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1851.991084
X-RAY DIFFRACTIONr_mcbond_other1.1651.9811080
X-RAY DIFFRACTIONr_mcangle_it2.0112.9591346
X-RAY DIFFRACTIONr_mcangle_other2.012.9611347
X-RAY DIFFRACTIONr_scbond_it1.3222.1161126
X-RAY DIFFRACTIONr_scbond_other1.3212.1181127
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1623.1271651
X-RAY DIFFRACTIONr_long_range_B_refined5.08924.3282473
X-RAY DIFFRACTIONr_long_range_B_other5.08824.3492474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 111 -
Rwork0.267 2141 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.115 Å / Origin y: 9.812 Å / Origin z: 43.928 Å
111213212223313233
T0.1814 Å20.0199 Å2-0.0075 Å2-0.083 Å2-0.017 Å2--0.0136 Å2
L0.7021 °20.2006 °20.0593 °2-0.0945 °20.1108 °2--0.5921 °2
S-0.0638 Å °0.0219 Å °-0.0346 Å °-0.0196 Å °0.0193 Å °-0.0157 Å °-0.0377 Å °-0.0541 Å °0.0445 Å °

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