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- PDB-4z84: PKAB3 in complex with pyrrolidine inhibitor 34a -

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Basic information

Entry
Database: PDB / ID: 4z84
TitlePKAB3 in complex with pyrrolidine inhibitor 34a
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase inhibitor alpha
KeywordsTRANSFERASE / inhibitor / protein kinase / structure-guided
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 / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / negative regulation of cAMP/PKA signal transduction / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / negative regulation of cAMP-dependent protein kinase activity / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of protein import into nucleus / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / 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. / 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
METHANOL / Chem-NVX / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.554 Å
AuthorsLund, B.A. / Alam, K.A. / Engh, R.A.
CitationJournal: Chemistry / Year: 2016
Title: Addressing the Glycine-Rich Loop of Protein Kinases by a Multi-Facetted Interaction Network: Inhibition of PKA and a PKB Mimic.
Authors: Lauber, B.S. / Hardegger, L.A. / Asraful, A.K. / Lund, B.A. / Dumele, O. / Harder, M. / Kuhn, B. / Engh, R.A. / Diederich, F.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 10, 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

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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
I: cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4735
Polymers43,0552
Non-polymers4183
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-7 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.852, 78.431, 79.506
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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: 40828.645 Da / Num. of mol.: 1 / Mutation: V123A, L173M, Q181K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00517, 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.) Homo sapiens (human) / References: UniProt: P61925
#3: Chemical ChemComp-NVX / 7-[(3S,4R)-4-(3-chlorophenyl)carbonylpyrrolidin-3-yl]-3H-quinazolin-4-one


Mass: 353.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClN3O2
#4: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The droplets, containing 16 mg/ml protein 25 mM Bis-Tris-HCl, pH 7.0, 150 mM KCl, 1.5mM octanoyl-N-methylglucamide, 0.8 mM PKI peptide and 1mM of the pyrrolidine inhibitor 34a, were ...Details: The droplets, containing 16 mg/ml protein 25 mM Bis-Tris-HCl, pH 7.0, 150 mM KCl, 1.5mM octanoyl-N-methylglucamide, 0.8 mM PKI peptide and 1mM of the pyrrolidine inhibitor 34a, were equilibrated against 12-26 % (v/v) methanol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.554→19.608 Å / Num. obs: 51501 / % possible obs: 91.46 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.7097396792 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 5.94
Reflection shellResolution: 1.5543→1.5931 Å / Num. unique all: 1855 / % possible all: 0.49

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSJanuary 10, 2014data reduction
XDSJanuary 10, 2014data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q61

1q61


Resolution: 1.554→19.60775 Å / SU ML: 0.230540808892 / Cross valid method: FREE R-VALUE / σ(F): 1.33870116593 / Phase error: 29.1829155833
RfactorNum. reflection% reflection
Rfree0.23429993529 1985 3.85429409138 %
Rwork0.208221335319 49516 -
obs0.209273093362 51501 91.4581520484 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.9211444025 Å2
Refinement stepCycle: LAST / Resolution: 1.554→19.60775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 29 457 3349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009965293454283000
X-RAY DIFFRACTIONf_angle_d1.101377850184068
X-RAY DIFFRACTIONf_chiral_restr0.0447435485971433
X-RAY DIFFRACTIONf_plane_restr0.00591263473264541
X-RAY DIFFRACTIONf_dihedral_angle_d13.6228584421101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5543-1.59310.389421305699710.3858116166521855X-RAY DIFFRACTION48.5016368673
1.5931-1.63620.357809797233970.3619785581712618X-RAY DIFFRACTION68.4051398337
1.6362-1.68430.3503827896521200.329028037783027X-RAY DIFFRACTION79.7920892495
1.6843-1.73870.3362446499541390.3120178994383410X-RAY DIFFRACTION89.0142964635
1.7387-1.80080.2719070011451510.283788318413751X-RAY DIFFRACTION98.212937327
1.8008-1.87280.3092935307061480.2711361168313849X-RAY DIFFRACTION99.9000249938
1.8728-1.9580.3157489819891590.2701274001363776X-RAY DIFFRACTION98.4981226533
1.958-2.06110.2346298484541510.2254882530523844X-RAY DIFFRACTION99.8500374906
2.0611-2.19010.2491273174031560.2137753581543842X-RAY DIFFRACTION99.6510468594
2.1901-2.35890.2766126256331530.2124551136013809X-RAY DIFFRACTION99.4228356336
2.3589-2.59580.2401159020891590.2031183535113886X-RAY DIFFRACTION99.7533908755
2.5958-2.97030.2332194184721560.2006974508443874X-RAY DIFFRACTION99.4325191216
2.9703-3.7380.1930215143631590.1799801077113910X-RAY DIFFRACTION99.2197025116
3.738-19.60930.1872864187521660.1641583891814065X-RAY DIFFRACTION99.2959399202
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)
10.82492185647-0.1013988410540.1315529260430.590113939195-0.04552498873350.3442199362940.02363915085080.0671732332489-0.0335043331367-0.1220282716620.0720184762766-0.3186343700390.342460520543-0.08064830730640.08682962974940.278711098775-0.0079082122489-0.05431356812480.259481180724-0.08478325615330.272241887986-17.7054208921-21.40257436251.81797999344
20.250304243638-0.09058732176160.1754952974240.3059515708980.09589671279210.214110508438-0.0395077475594-0.12566384284-0.07853037569460.0649107433307-0.0972016584810.1240988679660.0937611328298-0.2197739582521.50443952934E-50.244371888577-0.1001566131790.002990549477990.3776017705590.003836818708780.28138383225-36.7426474706-12.750296903316.9252186141
30.242740806244-0.1017000678280.1500945568360.0405597103571-0.08707458745910.4226003418970.130723245025-0.396755046499-0.0230037302570.1431174345720.04943168662350.2233738752190.22142295494-0.3243968421260.02056123919310.222066859956-0.07099580042210.008915278067420.3838278335610.007921096447940.262470754336-35.7987275367-10.895556373218.8695597334
40.475446388180.3581413192520.00838093048680.379532381390.01024481638810.0008821857901290.0247073799750.02291800533060.086323536269-0.06495335852720.01670229442130.07538035423350.105022465793-0.139635241508-7.47546936443E-50.188626243464-0.00716272778073-0.01423226622170.163177365844-0.008739485021340.179221917721-26.9800860185-11.52436838759.24843421067
50.3915580651-0.006492922373110.2064523922220.4459652885970.2839430885960.3053479425070.0493667458869-0.0986989458578-0.08170962827970.07739420999360.02248927032830.03272808962410.161300416753-0.1099407153410.001464570415880.188759511771-0.00442737540576-0.004062609024940.1775933335670.01525666893850.138180294344-16.9036288918-12.113623370119.900760125
60.422604371716-0.04013869713070.19087241150.1023232048150.07449033814820.143121198743-0.03283688300420.09593300313080.0763483322563-0.03357434085690.0229854564796-0.0251779471173-0.04242613758830.0469865543561-1.6583949711E-50.168963142921-0.00412607703519-0.0002353067174750.1438285061570.00819541556120.144604002768-12.4823467957-2.4537983586711.4452360554
70.5519254415830.2163344585970.3698951666730.3524469422620.006202624265320.30747926038-0.0433378348251-0.0473107897720.07499880079590.0887697653965-0.0375662471668-0.175910091405-0.1434275346150.182339243755-0.0006268795325570.1914227916880.0104145532128-0.01295828892220.179057345045-0.001424864566890.1945800548-1.659387536771.9409167464321.9560528717
80.929982515514-0.0571571324380.8883612813820.742476857750.1342910683560.9086640465410.02014989788810.176177013256-0.145849944879-0.1546578617540.0307522120111-0.1713069160940.1109603914350.1304605772190.001629368105620.1745253004870.0442734704990.01363322642960.164982810169-0.0282625174790.197264581745-2.88060413682-15.21434971415.3829770996
90.538469139460.491343212706-0.04115248035370.575258129847-0.1258240451960.05960188418180.0998884594763-0.2384486262410.1211739014220.150409311063-0.172483002217-0.03495310965390.180812621229-0.07480660628270.0002188492532340.261098425961-0.01892411892560.01756272323970.410265824434-0.01989905971240.26395295622-36.4562797077-7.4185736440519.2973264775
100.06085743119140.009041339033450.01670213586590.0207576678652-0.01588674884760.0527638476291-0.001522040443260.203455300175-0.09311167928480.01094783453850.091857460858-0.0494666179448-0.2077238904890.1913949557490.0003417100336840.2194096743920.004615366582290.004708245859060.259309480602-0.01564830358910.20699444234-6.586555054354.4695728662834.450770549
110.0300893039954-0.03446878189040.05222006763430.108601234986-0.04163664199140.09063607601960.0808949547490.1833964527430.1363834939440.0149185587193-0.1313994826920.1545430349160.0645749247859-0.1567803352811.18419221814E-50.2067162713930.009247703181980.001357242179380.250057549263-0.0222386058840.192661625567-18.47021586943.9089296421323.2268281225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 81 )
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 179 )
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 233 )
7X-RAY DIFFRACTION7chain 'A' and (resid 234 through 272 )
8X-RAY DIFFRACTION8chain 'A' and (resid 273 through 317 )
9X-RAY DIFFRACTION9chain 'A' and (resid 318 through 350 )
10X-RAY DIFFRACTION10chain 'I' and (resid 65 through 73 )
11X-RAY DIFFRACTION11chain 'I' and (resid 123 through 329 )

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