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- PDB-3poo: human cAMP-dependent protein kinase in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 3poo
Titlehuman cAMP-dependent protein kinase in complex with an inhibitor
Components
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
  • cAMP-dependent protein kinase inhibitor alphaCAMP-dependent pathway
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ATP Binding / Phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / mitochondrial protein catabolic process / ROBO receptors bind AKAP5 / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / mitochondrial protein catabolic process / ROBO receptors bind AKAP5 / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / sperm capacitation / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / cAMP-dependent protein kinase activity / ciliary base / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / regulation of cardiac conduction / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / sperm flagellum / Mitochondrial protein degradation / regulation of macroautophagy / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / protein kinase A signaling / Recruitment of NuMA to mitotic centrosomes / cellular response to epinephrine stimulus / calcium channel complex / Anchoring of the basal body to the plasma membrane / regulation of cytosolic calcium ion concentration / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / Regulation of insulin secretion / neural tube closure / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / Vasopressin regulates renal water homeostasis via Aquaporins / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / cellular response to heat / manganese ion binding / Factors involved in megakaryocyte development and platelet production / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. / 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
(2S,3S)-butane-2,3-diol / Chem-S69 / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKoester, H. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: fragment based drug design on PKA
Authors: Koester, H. / Craan, T. / Heine, A. / Klebe, G.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4394
Polymers43,0352
Non-polymers4042
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-4 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.870, 74.940, 79.700
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 catalytic subunit alpha / CAMP-dependent pathway / PKA C-alpha


Mass: 40808.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKACA, PRKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / CAMP-dependent pathway / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: unp residues 6-25 / Source method: obtained synthetically / References: UniProt: P61925
#3: Chemical ChemComp-S69 / N'-[(E)-(2,4-dihydroxy-6-methylphenyl)methylidene]-2-(3-methoxyphenyl)acetohydrazide


Mass: 314.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N2O4
#4: Chemical ChemComp-BUD / (2S,3S)-butane-2,3-diol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 5mM MES, 5mM BisTris-propane, 75mM LiCl, 1ml DTT, 0.1mM EDTA equilibrated against water/ethanol, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 20, 2010 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 57573 / Num. obs: 57573 / % possible obs: 100 % / Redundancy: 3.4 % / Rsym value: 0.039 / Net I/σ(I): 26.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2857 / Rsym value: 0.496 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OEW

1oew


Resolution: 1.6→26.89 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 2744 5.02 %RANDOM
Rwork0.1858 ---
obs0.1872 54627 93.83 %-
all-54627 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.477 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6124 Å20 Å2-0 Å2
2---0.8266 Å20 Å2
3----2.7858 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 29 248 3107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062956
X-RAY DIFFRACTIONf_angle_d0.9934010
X-RAY DIFFRACTIONf_dihedral_angle_d12.3431072
X-RAY DIFFRACTIONf_chiral_restr0.069430
X-RAY DIFFRACTIONf_plane_restr0.005510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.2882280.2534716X-RAY DIFFRACTION86
1.6572-1.72350.27412550.22054801X-RAY DIFFRACTION89
1.7235-1.80190.21142810.20474992X-RAY DIFFRACTION91
1.8019-1.89690.22432910.18825010X-RAY DIFFRACTION92
1.8969-2.01570.22972420.17815299X-RAY DIFFRACTION96
2.0157-2.17130.20762790.17735391X-RAY DIFFRACTION98
2.1713-2.38970.1912870.17475373X-RAY DIFFRACTION97
2.3897-2.73520.22422900.18695408X-RAY DIFFRACTION97
2.7352-3.44490.2133020.19075486X-RAY DIFFRACTION98
3.4449-26.89360.20062890.17935407X-RAY DIFFRACTION93
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)
10.17760.2925-0.16510.91630.72250.8382-0.01530.05460.05350.0380.0648-0.3407-0.01660.3193-0.02410.0032-0.0226-0.03840.1539-0.00070.141135.300114.44954.9984
20.66290.3757-0.05431.39970.76091.6286-0.0511-0.0161-0.03330.1362-0.0183-0.13430.25390.06810.05920.05330.01260.01170.04920.01740.049524.7531.64423.2476
30.77490.3281-0.02361.69980.72862.1081-0.06270.0443-0.14220.14290.0439-0.15840.45580.13860.02350.21520.03950.02460.1459-0.00210.167327.3887-3.65510.717
40.0668-0.09520.03630.4596-0.15950.0986-0.0126-0.0252-0.0242-0.0082-0.1226-0.03590.0889-0.05020.11430.241-0.04480.03510.1932-0.00940.155813.9817-1.9426-10.4903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 14:72)
2X-RAY DIFFRACTION2(chain A and resid 73:251)
3X-RAY DIFFRACTION3(chain A and resid 252:350)
4X-RAY DIFFRACTION4(chain B and resid 1005:1022)

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