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- PDB-6bku: Crystal Structure of the Human CAMKK2B bound to GSK650394 -

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Basic information

Entry
Database: PDB / ID: 6bku
TitleCrystal Structure of the Human CAMKK2B bound to GSK650394
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 / calcium-mediated signaling ...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 / 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-DXV / FORMIC ACID / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCounago, R.M. / dos Reis, C.V. / de Souza, G.P. / 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 bound to GSK650394
Authors: Counago, R.M. / dos Reis, C.V. / de Souza, G.P. / Ramos, P.Z. / Drewry, D. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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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)33,5563
Polymers33,1271
Non-polymers4282
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Calcium/calmodulin-dependent protein kinase kinase 2
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)67,1116
Polymers66,2552
Non-polymers8574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2760 Å2
ΔGint-22 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.971, 72.971, 119.301
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
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) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-DXV / 2-cyclopentyl-4-(5-phenyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzoic acid


Mass: 382.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 20% PEG smear medium, 0.2M sodium formate, 0.1M sodium-potassium phosphate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2→19.97 Å / Num. obs: 20267 / % possible obs: 89.9 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.033 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.724 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1601 / CC1/2: 0.534 / Rpim(I) all: 0.579 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UYJ

5uyj


Resolution: 2→19.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.524 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23658 1012 5 %RANDOM
Rwork0.19271 ---
obs0.19483 19202 89.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.588 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0 Å2-0 Å2
2--0.81 Å2-0 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 32 102 2215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192161
X-RAY DIFFRACTIONr_bond_other_d0.0020.022003
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9662928
X-RAY DIFFRACTIONr_angle_other_deg0.92.9854650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6545265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.242590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91115368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.73157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
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_it2.4224.4361066
X-RAY DIFFRACTIONr_mcbond_other2.4214.4381067
X-RAY DIFFRACTIONr_mcangle_it3.526.641329
X-RAY DIFFRACTIONr_mcangle_other3.5186.6431330
X-RAY DIFFRACTIONr_scbond_it2.9524.7221094
X-RAY DIFFRACTIONr_scbond_other2.9414.7181093
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6526.9541600
X-RAY DIFFRACTIONr_long_range_B_refined6.1351.7942379
X-RAY DIFFRACTIONr_long_range_B_other6.12951.7842380
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 75 -
Rwork0.323 1525 -
obs--99.63 %

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