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- PDB-6y0b: Crystal structure of the cAMP-dependent protein kinase A cocrysta... -

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Basic information

Entry
Database: PDB / ID: 6y0b
TitleCrystal structure of the cAMP-dependent protein kinase A cocrystallized with quinazolin-4-amine and PKI (5-24)
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase inhibitor alpha
KeywordsTRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase
Function / homology
Function and homology information


negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus ...negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / 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 / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / acrosomal vesicle / protein export from nucleus / positive regulation of phagocytosis / 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 / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...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. / 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
quinazolin-4-amine / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsOebbeke, M. / Wienen-Schmidt, B. / 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
DepositionFeb 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 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 1.2Oct 9, 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

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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)43,5634
Polymers43,3402
Non-polymers2232
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: provided by PISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-1 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.066, 73.097, 107.640
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: 41113.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first aminoacid (G) is numbered as -2 -> Therefore Methionine is number 0. The last aminoacid is number 350.
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P63248
#3: Chemical ChemComp-1LQ / quinazolin-4-amine


Mass: 145.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 Mega 8, 10mM quinazolin-4-amine in DMSO, 0.5 mM PKI (5-24) and 22 % methanol (v/v)0.003 mL drop volume, 0. ...Details: 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 Mega 8, 10mM quinazolin-4-amine in DMSO, 0.5 mM PKI (5-24) and 22 % 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: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.64→45.47 Å / Num. obs: 51100 / % possible obs: 90.3 % / Redundancy: 4.1 % / Rsym value: 0.046 / Net I/σ(I): 17.67
Reflection shellResolution: 1.64→1.74 Å / Num. unique obs: 6824 / Rsym value: 0.522

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Processing

Software
NameVersionClassification
PHASERphasing
Coot0.89model building
PHENIX1.16refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F14

6f14


Resolution: 1.71→45.47 Å / SU ML: 0.1746 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.1265
RfactorNum. reflection% reflection
Rfree0.2122 2296 5 %
Rwork0.1793 --
obs0.1809 45904 91.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.79 Å2
Refinement stepCycle: LAST / Resolution: 1.71→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 15 333 3264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613079
X-RAY DIFFRACTIONf_angle_d0.8094184
X-RAY DIFFRACTIONf_chiral_restr0.0519445
X-RAY DIFFRACTIONf_plane_restr0.0054553
X-RAY DIFFRACTIONf_dihedral_angle_d15.10211825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.25511080.22462044X-RAY DIFFRACTION70.19
1.75-1.790.2851270.22132413X-RAY DIFFRACTION82.76
1.79-1.840.28671280.21112437X-RAY DIFFRACTION82.77
1.84-1.890.27851240.20692355X-RAY DIFFRACTION80.62
1.89-1.940.23711320.19992508X-RAY DIFFRACTION85.08
1.94-20.22381400.20042654X-RAY DIFFRACTION90.33
2-2.080.23421420.19522699X-RAY DIFFRACTION91.56
2.08-2.160.22941470.19132796X-RAY DIFFRACTION95.49
2.16-2.260.23991490.1872840X-RAY DIFFRACTION96.3
2.26-2.380.22991510.19132873X-RAY DIFFRACTION97.64
2.38-2.520.23061550.1912936X-RAY DIFFRACTION98.28
2.52-2.720.21661550.19382954X-RAY DIFFRACTION99.62
2.72-2.990.22881570.18832971X-RAY DIFFRACTION99.71
2.99-3.430.20511570.17552987X-RAY DIFFRACTION99.24
3.43-4.320.18151590.14873011X-RAY DIFFRACTION99.19
4.32-45.470.16921650.15963130X-RAY DIFFRACTION98.45
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)
15.77994561388-1.59375650498-3.159790754851.969140587271.293009098735.587640746340.3079714619410.5792192241560.251615084976-0.254048486947-0.18969618855-0.00312073670328-0.474669224249-0.135770927149-0.1249233261590.1809953930380.0271949983875-0.02444316142470.1953366136880.0483189165080.24249464556-9.15766876465-8.914349551550.984226429263
20.9943754466380.173496459704-1.180934833647.55308224701-0.8970758419953.750406943810.0589551905407-0.1621160820860.4889805808810.3130197032960.09152884457540.186761094636-0.0049168863968-0.13546974007-0.0910660722840.2055281601840.0343073968520.005957330552840.3321940266890.04696219154730.432467567488-25.8769368298-23.935502676229.854867715
32.771048920852.38113865189-0.8190162515535.015953711170.4043563327833.518450576230.25065819096-0.402073454934-0.02186960371080.656992663975-0.08560182379-0.213290991632-0.007262239740510.167056772467-0.167475991910.1889694324920.02237742421460.01733839795770.258610419758-0.02045029006180.209927747228-17.1387567819-13.692121450831.5288467697
40.8822817447620.010120284720.05652172605741.17574771234-0.04648305945770.6013838962290.023847037704-0.0857246677845-0.06280520505930.0799802197363-0.01376448658080.1597776415560.0233869895365-0.1077073405610.00762697565280.110514389301-0.01843382358870.005017538982660.1356335655290.004305174030670.116282950333-10.6850959872-22.471393223919.0322378982
54.054581503993.125273075262.741982942584.831467302863.048569153034.04461284122-0.040398856865-0.1174187271410.2766813282930.109814119641-0.05375359366370.375923153688-0.263385960408-0.1701873529970.04325621363640.1882213577870.0331418101941-0.003351881204960.161436816694-0.05045226199720.161870052987-5.87044163599-9.6650471844722.9773917311
61.14605416814-0.4433923660060.02954977438382.434074029130.1526894569151.67586180821-0.0135074214849-0.05300384510090.1007513882480.178659238555-0.0192913355256-0.303055719458-0.06614355470220.1102041627950.02366450230250.0912325835317-0.0133594219292-0.01579009517940.1178499780120.005274480619950.1255324524878.64513160169-19.415961519920.3383707263
73.302270166340.5776870764710.875038357152.111231776830.4952121518712.255960322560.008021660969770.2973783248370.0501806271409-0.0837800970698-0.0141372468749-0.0340637779602-0.0897574419110.09871694909770.03485532861970.132816791370.01560692561440.0008311392177530.09545752861560.005809818788110.103263236475-0.0636612974993-18.63617200826.40618145851
83.53009296667-2.49727551021-2.773248885527.068486790193.654845802134.13011154132-0.0554460981544-0.609924930274-0.05143210949680.779105930020.0451976627862-0.01081708151610.4337201053760.2461413068790.03333604870680.245199403696-0.0326612576319-0.04145480621760.4263475654370.009904600798590.289768982104-20.4671243552-22.557939979634.5394723652
95.94963172262-1.412749630532.629199124645.01823275034.814545131068.299232304360.0723879256908-0.0339493861087-0.2227026028020.2713609682430.0617672691356-0.2738265218210.2084720550830.215610869898-0.1139582841160.1799842107240.01844629462230.004781767018820.186175683640.06370325056430.18022983627611.9020353676-33.703615071326.6881976913
109.08528582055-2.41888289146-0.2480899483872.78481195044-0.3580376485166.347394110010.158307669793-0.509042052250.04388834329010.542604922528-0.0175533860902-0.000386299698201-0.04700715220070.0343495558452-0.1591635651410.208957013415-0.01439183572840.007115583712040.1613061755960.04533335397530.10738941680.852904588462-24.217910479431.4857060888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 179 )
5X-RAY DIFFRACTION5chain 'A' and (resid 180 through 198 )
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 272 )
7X-RAY DIFFRACTION7chain 'A' and (resid 273 through 316 )
8X-RAY DIFFRACTION8chain 'A' and (resid 317 through 350 )
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 13 )
10X-RAY DIFFRACTION10chain 'B' and (resid 14 through 23 )

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