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- PDB-3aqv: Human AMP-activated protein kinase alpha 2 subunit kinase domain ... -

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Basic information

Entry
Database: PDB / ID: 3aqv
TitleHuman AMP-activated protein kinase alpha 2 subunit kinase domain (T172D) complexed with compound C
Components5'-AMP-activated protein kinase catalytic subunit alpha-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Transferase / Signaling protein / Serine/threonine protein kinase / Phosphorylation / ATP-binding / Nucleotide-binding / Cholesterol biosynthesis / Fatty acid biosynthesis / Lipid synthesis / glucose metabolism / Magnesium / Metal-binding / Serine/threonine-protein kinase / Steroid biosynthesis / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / Energy dependent regulation of mTOR by LKB1-AMPK ...[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of TOR signaling / negative regulation of hepatocyte apoptotic process / Carnitine metabolism / nucleotide-activated protein kinase complex / protein localization to lipid droplet / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / Nuclear events mediated by NFE2L2 / lipid biosynthetic process / negative regulation of tubulin deacetylation / Macroautophagy / AMP-activated protein kinase activity / positive regulation of protein localization / cholesterol biosynthetic process / cellular response to nutrient levels / positive regulation of macroautophagy / fatty acid homeostasis / regulation of macroautophagy / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / energy homeostasis / negative regulation of TORC1 signaling / cellular response to calcium ion / protein serine/threonine/tyrosine kinase activity / positive regulation of glycolytic process / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / TP53 Regulates Metabolic Genes / regulation of circadian rhythm / Wnt signaling pathway / autophagy / cytoplasmic stress granule / cellular response to prostaglandin E stimulus / fatty acid biosynthetic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / cellular response to oxidative stress / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / axon / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / neuronal cell body / chromatin binding / negative regulation of apoptotic process / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-TAK / 5'-AMP-activated protein kinase catalytic subunit alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsHanda, N. / Takagi, T. / Saijo, S. / Kishishita, S. / Toyama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural basis for compound C inhibition of the human AMP-activated protein kinase alpha 2 subunit kinase domain
Authors: Handa, N. / Takagi, T. / Saijo, S. / Kishishita, S. / Takaya, D. / Toyama, M. / Terada, T. / Shirouzu, M. / Suzuki, A. / Lee, S. / Yamauchi, T. / Okada-Iwabu, M. / Iwabu, M. / Kadowaki, T. / ...Authors: Handa, N. / Takagi, T. / Saijo, S. / Kishishita, S. / Takaya, D. / Toyama, M. / Terada, T. / Shirouzu, M. / Suzuki, A. / Lee, S. / Yamauchi, T. / Okada-Iwabu, M. / Iwabu, M. / Kadowaki, T. / Minokoshi, Y. / Yokoyama, S.
History
DepositionNov 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-AMP-activated protein kinase catalytic subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9712
Polymers31,5721
Non-polymers3991
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.476, 70.476, 130.508
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 5'-AMP-activated protein kinase catalytic subunit alpha-2 / AMPK subunit alpha-2


Mass: 31571.730 Da / Num. of mol.: 1 / Fragment: kinase domain / Mutation: T172D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PX060824-01 / Production host: Cell-free protein synthesis
References: UniProt: P54646, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-TAK / 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine / Dorsomorphin


Mass: 399.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.1M Bis-Tris (pH 6.5), 1.5M ammonium sulfate, 0.1M NaCl, 0.5mM Compound C, 5mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 20469 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.072 / Net I/σ(I): 34.2
Reflection shellResolution: 2.08→2.19 Å / Mean I/σ(I) obs: 8.14 / Rsym value: 0.409 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YZA

2yza


Resolution: 2.08→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.069 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28062 1044 5.1 %RANDOM
Rwork0.22133 ---
obs0.22423 19340 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.441 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.08→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 30 112 2301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222245
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.9773030
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3645265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6623.137102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30715397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9581515
X-RAY DIFFRACTIONr_chiral_restr0.1630.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211680
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.351.51326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31122146
X-RAY DIFFRACTIONr_scbond_it3.3933919
X-RAY DIFFRACTIONr_scangle_it5.2984.5884
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.081→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 73 -
Rwork0.213 1382 -
obs--98.78 %

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