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- PDB-5n3c: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n3c
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule Thiophene-3-Carboximidamide
Components
  • cAMP dependent protein kinase inhibitor alpha-like protein
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / fragment / complex / serine threonine kinase / cAMP / kinase / PKA
Function / homology
Function and homology information


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 / regulation of osteoblast differentiation / cellular response to cold ...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 / 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 / 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 / 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. / 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
[azanyl(thiophen-3-yl)methylidene]azanium / UPF0418 protein FAM164A / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.772 Å
AuthorsSiefker, C. / Heine, A. / Klebe, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts.
Authors: Oebbeke, M. / Siefker, C. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 17, 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 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4324
Polymers43,1872
Non-polymers2452
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-13 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.513, 72.728, 108.550
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 / PKA C-alpha


Mass: 41193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylation of S11, S140, T198 and S339 / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP dependent protein kinase inhibitor alpha-like protein


Mass: 1993.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cAMP dependent protein kinase inhibitor peptide / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48*PLUS
#3: Chemical ChemComp-8M2 / [azanyl(thiophen-3-yl)methylidene]azanium


Mass: 127.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N2S
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: MES-BIS-TRIS Mega8-Solution DTT EDTA LiCl Methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2016 / Details: Silicon
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 45623 / % possible obs: 99.8 % / Redundancy: 6.58 % / CC1/2: 0.99 / Rrim(I) all: 0.109 / Net I/σ(I): 13.24
Reflection shellResolution: 1.77→1.88 Å / Redundancy: 6.41 % / Mean I/σ(I) obs: 3.06 / Num. unique obs: 7178 / CC1/2: 0.87 / Rrim(I) all: 0.595 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WIH

4wih


Resolution: 1.772→45.59 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.22
RfactorNum. reflection% reflection
Rfree0.1958 2281 5 %
Rwork0.1782 --
obs0.1791 45616 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.772→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 16 235 3117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073074
X-RAY DIFFRACTIONf_angle_d0.8944189
X-RAY DIFFRACTIONf_dihedral_angle_d14.0421832
X-RAY DIFFRACTIONf_chiral_restr0.054446
X-RAY DIFFRACTIONf_plane_restr0.006547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7723-1.81080.2631370.2682604X-RAY DIFFRACTION97
1.8108-1.85290.30061380.25972633X-RAY DIFFRACTION100
1.8529-1.89930.31211430.27762704X-RAY DIFFRACTION100
1.8993-1.95060.25881410.23942684X-RAY DIFFRACTION100
1.9506-2.0080.23831400.19632669X-RAY DIFFRACTION100
2.008-2.07290.21911420.18812701X-RAY DIFFRACTION100
2.0729-2.14690.24081410.17652665X-RAY DIFFRACTION100
2.1469-2.23290.17391410.16542683X-RAY DIFFRACTION100
2.2329-2.33450.17721430.16062721X-RAY DIFFRACTION100
2.3345-2.45760.16351420.15842706X-RAY DIFFRACTION100
2.4576-2.61160.17251420.16022682X-RAY DIFFRACTION100
2.6116-2.81320.17561430.16442728X-RAY DIFFRACTION100
2.8132-3.09620.19111440.16552724X-RAY DIFFRACTION100
3.0962-3.54410.18411440.17042739X-RAY DIFFRACTION100
3.5441-4.46460.16751460.15482787X-RAY DIFFRACTION100
4.4646-45.60480.19711540.18822905X-RAY DIFFRACTION100
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)
10.35-0.086-0.26310.262-0.09730.2179-0.0783-0.2185-0.10980.0286-0.00650.08060.18690.3284-0.03770.1476-0.12090.06830.3325-0.02740.1564-8.91438.1895-1.6065
20.44080.1908-0.01690.30240.32240.57920.1810.3528-0.0649-0.5624-0.00310.6052-0.3482-0.11280.29210.13-0.0143-0.20050.32720.02830.4818-23.351323.2819-31.297
30.6181-0.37850.17210.865-0.34180.14340.11180.1817-0.0404-0.1115-0.05040.23450.0242-0.05670.05720.10760.0067-0.04520.1785-0.02760.1389-14.418919.8678-25.679
40.1756-0.03810.08390.0914-0.01770.0617-0.0095-0.05990.02120.1434-0.00070.01120.0183-0.1595-0.02220.1444-0.02510.02280.10080.00010.0854-5.079218.7737-10.4384
50.46340.16090.29960.75290.11770.323-0.00240.07890.0297-0.0140.013-0.04870.01240.015-0.00210.0917-0.0117-0.00150.06010.00340.08120.938417.1104-22.2817
60.39670.09210.29890.55850.25160.46090.012-0.0966-0.01030.2987-0.0238-0.11730.09570.0229-0.11550.1564-0.0049-0.01930.09250.00920.09384.460619.8435-7.8903
70.5564-0.0114-0.29120.3289-0.02060.49210.44110.53040.0321-0.4581-0.17860.1655-0.08710.04880.64690.24680.121-0.22820.3339-0.02530.2786-19.098422.8421-34.8019
80.0523-0.0520.02490.0348-0.02010.02910.18290.20380.0237-0.2581-0.2232-0.17760.29920.1248-0.00060.25850.0194-0.01440.14260.0250.18060.86322.7832-31.5573
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 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 140 )
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 160 )
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 251 )
6X-RAY DIFFRACTION6chain 'A' and (resid 252 through 316 )
7X-RAY DIFFRACTION7chain 'A' and (resid 317 through 350 )
8X-RAY DIFFRACTION8chain 'B' and (resid 13 through 25 )

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