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- PDB-6you: Crystal structure of the cAMP-dependent protein kinase A in compl... -

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Basic information

Entry
Database: PDB / ID: 6you
TitleCrystal structure of the cAMP-dependent protein kinase A in complex with Pyrido[3,2-d]pyrimidin-4-amine (soaked)
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase
Function / homology
Function and homology information


cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / cellular response to parathyroid hormone stimulus / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation ...cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / cellular response to parathyroid hormone stimulus / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / positive regulation of gluconeogenesis / acrosomal vesicle / positive regulation of phagocytosis / protein export from nucleus / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / positive regulation of insulin secretion / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / 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 catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
pyrido[3,2-d]pyrimidin-4-amine / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsOebbeke, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Fragment based drug design - Small chemical changes of fragments effecting big changes in binding
Authors: Oebbeke, M. / Wienen-Schmidt, B. / Gerber, H.-D. / Heine, A. / Klebe, G.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3402
Polymers41,1941
Non-polymers1461
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.895, 71.446, 97.445
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 41193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Chemical ChemComp-P4Q / pyrido[3,2-d]pyrimidin-4-amine


Mass: 146.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0,2 mM PKA in 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8 and 23 % methanol (v/v) 0.003 mL drop volume, 0.5 mL reservoir volume

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.73→45.805 Å / Num. obs: 37845 / % possible obs: 98.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.69 Å2 / Rsym value: 0.063 / Net I/σ(I): 14.92
Reflection shellResolution: 1.73→1.83 Å / Mean I/σ(I) obs: 2.74 / Num. unique obs: 5976 / Rsym value: 0.49 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.16refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F14

6f14


Resolution: 1.73→45.8 Å / SU ML: 0.1758 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6117
RfactorNum. reflection% reflection
Rfree0.2164 1892 5 %
Rwork0.1791 --
obs0.181 37823 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.94 Å2
Refinement stepCycle: LAST / Resolution: 1.73→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 11 233 2954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612849
X-RAY DIFFRACTIONf_angle_d0.76773873
X-RAY DIFFRACTIONf_chiral_restr0.0521412
X-RAY DIFFRACTIONf_plane_restr0.005510
X-RAY DIFFRACTIONf_dihedral_angle_d15.42911687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.24621260.21032410X-RAY DIFFRACTION94.77
1.77-1.820.27571350.20482555X-RAY DIFFRACTION99.74
1.82-1.870.24161360.20242594X-RAY DIFFRACTION99.78
1.87-1.930.36621300.25422465X-RAY DIFFRACTION95.47
1.93-20.25811340.19412527X-RAY DIFFRACTION97.94
2-2.080.22441350.17762577X-RAY DIFFRACTION99.2
2.08-2.180.20391350.16642566X-RAY DIFFRACTION99.48
2.18-2.290.24741330.19842509X-RAY DIFFRACTION96.46
2.29-2.440.2191360.17152601X-RAY DIFFRACTION99.56
2.44-2.630.26281370.1862593X-RAY DIFFRACTION98.63
2.63-2.890.21611360.18882584X-RAY DIFFRACTION98.87
2.89-3.310.18931390.17692638X-RAY DIFFRACTION99.61
3.31-4.170.18811370.15522599X-RAY DIFFRACTION97.3
4.17-45.80.18481430.16932713X-RAY DIFFRACTION96.42
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)
10.391677015069-0.133724939688-0.01898367626940.473628097047-0.04966073396270.007928737310510.05055139074340.005607060510870.0311298310999-0.0408317264368-0.0636104217767-0.0270643729524-0.06554874185160.0232429349519-3.20414945308E-50.17157754651-0.03316781045840.0220049759510.1394947309060.004600776036630.17106875748518.907534579116.179736831219.2040093447
20.24993088706-0.0575079257542-0.3514605400430.2805508091270.2131356552640.5375203115110.0224399749971-0.00146773276591-0.0114426517618-0.0616741647385-0.0462112845968-0.00859070110096-0.048252569992-0.000349646765458-0.000851733899750.1320043531750.0176763599775-0.005122186226570.129056931687-0.007979764242890.13305895410813.19878411888.301711702221.0703004093
30.581030775704-0.255068335891-0.06841174562330.784284162582-0.3405369486030.6387788973330.0314198084504-0.02833855224570.01622777938350.007210634592870.00951540884010.0484097408588-0.0543687796772-0.04008460920460.0005557674168110.1079267391430.0129713940306-0.005363528472660.122664921321-0.005823474136250.122064016494-0.087187194941511.562366532233.6999373031
40.346836408772-0.246506653352-0.3549431676390.6504045573580.4382670139790.434553710433-0.003317720766050.01114982137360.0152352330094-0.0998224358218-0.061912814714-0.00935799141237-0.0122395337367-0.0464125032067-7.02946938815E-50.141878605417-0.0183264776692-0.008355299535910.1578318929090.01675644836970.16858387792815.28052819084.7573115557820.0255940677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 297 )
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 350 )

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