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- PDB-5n3f: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n3f
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule N-[3-(aminomethyl)phenyl]acetamide
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 / cellular response to cold / regulation of osteoblast differentiation ...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 / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / cellular response to glucagon stimulus / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / 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 / regulation of cell cycle / postsynapse / 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 / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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. / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
N-[3-(aminomethyl)phenyl]acetamide / 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: 1.68 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 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 1.2Jan 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 1.3Nov 20, 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)43,7526
Polymers43,1872
Non-polymers5654
Water4,324240
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-21 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.765, 72.194, 108.760
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 and T198 / 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-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-463 / N-[3-(aminomethyl)phenyl]acetamide


Mass: 164.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2016 / 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: 1.68→50 Å / Num. obs: 53011 / % possible obs: 99.9 % / Redundancy: 6.61 % / CC1/2: 1 / Rrim(I) all: 0.047 / Net I/σ(I): 24.97
Reflection shellResolution: 1.68→1.79 Å / Redundancy: 6.41 % / Mean I/σ(I) obs: 3.76 / Num. unique obs: 8418 / CC1/2: 0.87 / Rrim(I) all: 0.543 / % possible all: 99.7

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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: 1.68→45.575 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.25
RfactorNum. reflection% reflection
Rfree0.1929 2651 5 %
Rwork0.1724 --
obs0.1734 53003 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.68→45.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 40 240 2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172766
X-RAY DIFFRACTIONf_angle_d1.3553757
X-RAY DIFFRACTIONf_dihedral_angle_d13.8891621
X-RAY DIFFRACTIONf_chiral_restr0.105403
X-RAY DIFFRACTIONf_plane_restr0.01492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6842-1.71490.28541340.24832554X-RAY DIFFRACTION99
1.7149-1.74780.24321380.21092610X-RAY DIFFRACTION100
1.7478-1.78350.21351390.19082636X-RAY DIFFRACTION100
1.7835-1.82230.22581360.17832601X-RAY DIFFRACTION100
1.8223-1.86470.23631390.17792636X-RAY DIFFRACTION100
1.8647-1.91130.21251380.16392615X-RAY DIFFRACTION100
1.9113-1.9630.22661380.16082635X-RAY DIFFRACTION100
1.963-2.02080.20561390.16382639X-RAY DIFFRACTION100
2.0208-2.0860.1921380.15672610X-RAY DIFFRACTION100
2.086-2.16050.18381390.14772642X-RAY DIFFRACTION100
2.1605-2.2470.19291380.14982632X-RAY DIFFRACTION100
2.247-2.34930.17961400.15092645X-RAY DIFFRACTION100
2.3493-2.47320.17231400.15952664X-RAY DIFFRACTION100
2.4732-2.62810.16991380.16242634X-RAY DIFFRACTION100
2.6281-2.8310.17731410.17122671X-RAY DIFFRACTION100
2.831-3.11580.19671420.17372691X-RAY DIFFRACTION100
3.1158-3.56650.21241400.17172674X-RAY DIFFRACTION100
3.5665-4.49280.16591440.16322731X-RAY DIFFRACTION100
4.4928-45.59180.19771500.2032832X-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)
11.9609-0.5958-0.67521.59250.31441.2768-0.4137-0.1698-0.31210.14120.31160.30050.44980.01740.17940.2302-0.13060.14390.1781-0.04620.2444-12.27315.9305-4.7666
20.4490.0151-0.28420.49970.19090.26440.14080.66890.014-0.50420.06140.83980.0498-0.35680.32630.2374-0.0684-0.16850.5073-0.00280.5889-24.662224.2521-30.0806
32.1952-2.31320.30734.2633-0.87780.72910.50560.7551-0.0981-1.1847-0.4560.37330.32410.00760.06990.3677-0.0109-0.11630.4117-0.07640.2939-15.501413.4002-30.5136
40.4966-0.2803-0.33491.4146-0.54470.5241-0.00430.10620.092-0.0865-0.00890.27350.0028-0.2453-0.00010.1743-0.0281-0.01240.2141-0.00140.1745-10.201822.5556-17.9465
50.86960.06080.17121.69650.29721.38780.00550.0627-0.01750.0307-0.0134-0.11980.04510.0536-0.00470.1186-0.0198-0.00530.11910.01070.12873.795317.4288-18.1219
60.38460.06810.20440.6058-0.09980.4246-0.00830.10260.17330.09170.08650.3119-0.1034-0.22640.03780.2192-0.02110.02580.25340.01260.2481-12.178929.7015-13.6824
72.3784-0.0357-0.58580.78140.38370.34710.23190.28530.2555-0.4617-0.09820.01930.464-0.04440.21630.39470.0136-0.05050.23240.02890.1451.123722.9757-31.4084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 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 160 )
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 297 )
6X-RAY DIFFRACTION6chain 'A' and (resid 298 through 333 )
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 25 )

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