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- PDB-5n1d: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n1d
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule N-methyl-1-(5-pyridin-3-yloxyfuran-2-yl)methanamine
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase inhibitor alpha-like protein
KeywordsTRANSFERASE / fragment / complex / serine threonine kinase / cAMP / kinase / PKA
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 / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / 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 / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / 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 / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / ATP binding / nucleus / 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. / 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
(5-pyridin-3-yloxyfuran-2-yl)methanamine / cAMP-dependent protein kinase inhibitor / 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: 1.609 Å
AuthorsSiefker, C. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: A crystallographic fragment study with cAMP-dependent protein kinase A
Authors: Siefker, C. / Heine, A. / Klebe, G.
History
DepositionFeb 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Oct 16, 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)43,6525
Polymers43,2252
Non-polymers4273
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-29 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.612, 73.456, 108.703
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: 41113.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylation of S11, T198 and S339 / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Plasmid: pET-16bTEV / 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: 2111.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cAMP dependent protein kinase inhibitor peptide / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A061IH64, UniProt: G3HK48*PLUS
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-8FZ / (5-pyridin-3-yloxyfuran-2-yl)methanamine


Mass: 190.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.88 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: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2015 / Details: Silicon, active surface
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 61272 / % possible obs: 99.4 % / Redundancy: 4.79 % / CC1/2: 0.99 / Rrim(I) all: 0.07 / Net I/σ(I): 17.23
Reflection shellResolution: 1.61→1.71 Å / Redundancy: 4.61 % / Num. unique obs: 9718 / CC1/2: 0.82 / % possible all: 98.5

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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: 1.609→45.815 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1857 3064 5 %
Rwork0.1554 --
obs0.1569 61267 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.609→45.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 30 392 3380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173226
X-RAY DIFFRACTIONf_angle_d1.4754393
X-RAY DIFFRACTIONf_dihedral_angle_d15.6871947
X-RAY DIFFRACTIONf_chiral_restr0.079462
X-RAY DIFFRACTIONf_plane_restr0.011583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6093-1.63450.24531340.22932551X-RAY DIFFRACTION96
1.6345-1.66130.23711370.21142602X-RAY DIFFRACTION99
1.6613-1.68990.2811370.20292609X-RAY DIFFRACTION99
1.6899-1.72070.21341370.1852584X-RAY DIFFRACTION99
1.7207-1.75380.2011380.17832634X-RAY DIFFRACTION99
1.7538-1.78960.19071370.16922601X-RAY DIFFRACTION99
1.7896-1.82850.18821370.1662610X-RAY DIFFRACTION100
1.8285-1.8710.21121380.16252621X-RAY DIFFRACTION100
1.871-1.91780.19241380.16272619X-RAY DIFFRACTION99
1.9178-1.96970.21421380.16812618X-RAY DIFFRACTION99
1.9697-2.02760.17571390.15692639X-RAY DIFFRACTION100
2.0276-2.09310.21461390.15712640X-RAY DIFFRACTION100
2.0931-2.16790.17861380.14772632X-RAY DIFFRACTION100
2.1679-2.25470.1781390.14152643X-RAY DIFFRACTION100
2.2547-2.35730.14981400.13762643X-RAY DIFFRACTION100
2.3573-2.48150.15591390.142646X-RAY DIFFRACTION100
2.4815-2.6370.18341400.14182657X-RAY DIFFRACTION100
2.637-2.84060.18961400.15232673X-RAY DIFFRACTION100
2.8406-3.12640.19461430.1532701X-RAY DIFFRACTION100
3.1264-3.57860.16821410.15372695X-RAY DIFFRACTION100
3.5786-4.50810.16331450.13852739X-RAY DIFFRACTION100
4.5081-45.83330.19661500.16562846X-RAY DIFFRACTION99
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)
10.52970.254-0.22920.62610.08730.1710.08180.2757-0.2315-0.0759-0.00440.0710.2564-0.0608-0.01290.1660.04290.01590.21940.00730.18059.657882.00521.5695
20.13390.3082-0.00071.3549-0.5630.43240.2448-0.4217-0.04820.6304-0.1138-0.4801-0.05290.13080.07560.20960.0102-0.03740.2846-0.06290.360525.838797.65230.13
30.2815-0.10690.06510.4768-0.07050.01580.1827-0.2835-0.05260.5133-0.0979-0.08510.02850.08410.01030.2718-0.052-0.02550.27540.00850.15816.923286.834331.6516
40.7142-0.124-0.08910.65920.08160.15730.0336-0.06390.10630.0657-0.0294-0.1147-0.01570.0854-0.00030.1183-0.0082-0.00950.1169-0.0080.122910.810896.027118.8842
50.2791-0.015-0.30560.1044-0.07970.34920.0655-0.143-0.04230.1213-0.049-0.09040.05210.22330.06450.1870.01120.00770.15660.03270.13756.011882.06522.9166
61.0564-0.1284-0.09681.03810.04390.878-0.0030.0459-0.05060.0174-0.03530.07930.0595-0.1064-0.10870.1003-0.0087-0.00550.0884-0.00180.106-5.146392.291114.8132
70.74470.42880.35240.98250.0230.1430.0678-0.37450.09210.8309-0.0621-0.1469-0.1993-0.14580.02020.3143-0.0111-0.02670.3431-0.01820.272720.412495.487834.2347
80.0094-0.0030.0130.01660.00370.02540.1192-0.12730.0660.13430.04230.1235-0.1782-0.1158-00.19280.025-0.00290.1899-0.04240.185-11.9526107.64426.4047
90.707-0.1259-0.1730.15070.01160.05090.2577-0.22930.11080.2634-0.1322-0.13870.08690.08350.06280.2576-0.0158-0.00570.1645-0.03670.1247-1.563299.059631.3126
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 316 )
7X-RAY DIFFRACTION7chain 'A' and (resid 317 through 350 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 12 )
9X-RAY DIFFRACTION9chain 'B' and (resid 13 through 22 )

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