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- PDB-2uvx: Structure of PKA-PKB chimera complexed with 7-azaindole -

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Basic information

Entry
Database: PDB / ID: 2uvx
TitleStructure of PKA-PKB chimera complexed with 7-azaindole
Components
  • CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
  • CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT
KeywordsTRANSFERASE/INHIBITOR / CAMP / KINASE / MYRISTATE / TRANSFERASE / LIPOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE-INHIBITOR COMPLEX / NUCLEOTIDE-BINDING / PROTEIN KINASE INHIBITOR / ATP- BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION
Function / homology
Function and homology information


CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / Regulation of PLK1 Activity at G2/M Transition / PKA activation / Hedgehog 'off' state / MAPK6/MAPK4 signaling / negative regulation of cAMP-dependent protein kinase activity / GLI3 is processed to GLI3R by the proteasome / mesoderm formation / cAMP-dependent protein kinase inhibitor activity / histone H1-4S35 kinase activity / cAMP-dependent protein kinase / positive regulation of triglyceride catabolic process / cAMP-dependent protein kinase activity / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / Mitochondrial protein degradation / sperm capacitation / regulation of osteoblast differentiation / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / ciliary base / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / sperm flagellum / negative regulation of cAMP/PKA signal transduction / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / positive regulation of phagocytosis / acrosomal vesicle / regulation of proteasomal protein catabolic process / negative regulation of protein localization to chromatin / lipid droplet / cellular response to glucose stimulus / neuromuscular junction / regulation of microtubule cytoskeleton organization / positive regulation of cholesterol biosynthetic process / mRNA processing / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of cell cycle / protein kinase activity / postsynapse / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
1H-PYRROLO[2,3-B]PYRIDINE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDavies, T.G. / Donald, A. / McHardy, T. / Rowlands, M.G. / Hunter, L.J. / Boyle, R.G. / Aherne, G.W. / Garrett, M.D. / Collins, I.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Rapid Evolution of 6-Phenylpurine Inhibitors of Protein Kinase B Through Structure-Based Design
Authors: Donald, A. / Mchardy, T. / Rowlands, M.G. / Hunter, L.J. / Davies, T.G. / Berdini, V. / Boyle, R.G. / Aherne, G.W. / Garrett, M.D. / Collins, I.
History
DepositionMar 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT
I: CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1753
Polymers43,0572
Non-polymers1181
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-6.8 kcal/mol
Surface area19800 Å2
MethodPQS
Unit cell
Length a, b, c (Å)72.537, 74.400, 79.869
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 CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT / PROTEIN KINASE A / PKA C-ALPHA


Mass: 40830.617 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00517
#2: Protein/peptide CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA / PKI / PKI-ALPHA / MUSCLE/BRAIN ISOFORM


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-24 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61925
#3: Chemical ChemComp-GVH / 1H-PYRROLO[2,3-B]PYRIDINE


Mass: 118.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 104 TO THR ENGINEERED RESIDUE IN CHAIN A, VAL 123 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, VAL 104 TO THR ENGINEERED RESIDUE IN CHAIN A, VAL 123 TO ALA ENGINEERED RESIDUE IN CHAIN A, LEU 173 TO MET ENGINEERED RESIDUE IN CHAIN A, GLN 181 TO LYS
Has protein modificationY
Sequence details4 RESIDUES OF THE WILD-TYPE PKA SEQUENCE HAVE BEEN MUTATED TO THE CORRESPONDING RESIDUES IN PKB

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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: 2.31 Å3/Da / Density % sol: 46.34 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30.6 Å / Num. obs: 27518 / % possible obs: 97.5 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0019Grefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.32 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1466 5.1 %RANDOM
Rwork0.172 ---
obs0.175 27518 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---0.25 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 9 382 3332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223026
X-RAY DIFFRACTIONr_bond_other_d0.0010.022118
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9524082
X-RAY DIFFRACTIONr_angle_other_deg0.8652.9975129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82723.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45115.028540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0731518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02659
X-RAY DIFFRACTIONr_nbd_refined0.2070.2633
X-RAY DIFFRACTIONr_nbd_other0.1920.22259
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21487
X-RAY DIFFRACTIONr_nbtor_other0.0870.21520
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0810.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0280.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.10151777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.12862866
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.12661249
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1567.51216
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 117
Rwork0.232 1782

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