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- PDB-6i2b: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 6i2b
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus Griseus in complex with compounds RKp153 and RKp117
Components
  • UPF0418 protein FAM164A
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / Complex / peptidic ligand
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 / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / 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 / 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 / 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
Chem-9LQ / beta-D-ribopyranose / 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: 1.97 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: Acs Omega / Year: 2019
Title: Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage
Authors: Mueller, J.M. / Kirschner, R. / Geyer, A. / Klebe, G.
History
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMay 15, 2019ID: 6EMC
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 10, 2021Group: Advisory / Structure summary / Category: chem_comp / pdbx_database_PDB_obs_spr / Item: _chem_comp.pdbx_synonyms
Revision 1.3Mar 17, 2021Group: Advisory / Category: pdbx_database_PDB_obs_spr / Item: _pdbx_database_PDB_obs_spr.id
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
D: UPF0418 protein FAM164A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1075
Polymers43,1062
Non-polymers1,0013
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-0 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.726, 83.726, 60.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Tissue: Ovary / Gene: PRKACA / Organ: Ovary
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide UPF0418 protein FAM164A


Mass: 1912.092 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PKI 5-22 with T16RBT mutation. A ribose has been covalently attached to a threonine of the peptide
Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48
#3: Chemical ChemComp-9LQ / [2-[(4-isoquinolin-5-ylsulfonyl-1,4-diazepan-1-yl)methyl]phenyl]boronic acid


Mass: 425.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24BN3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM Mes-Bis-Tris, 75 mM lithium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 0.7 mM peptidic ligand, 5 mM RKp117, 15% v/v methanol/water in reservoir

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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: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.97→48.913 Å / Num. obs: 29620 / % possible obs: 99.4 % / Redundancy: 4.83 % / CC1/2: 0.999 / Rsym value: 0.04 / Net I/σ(I): 22.78
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 4.92 % / Mean I/σ(I) obs: 3.09 / Num. unique obs: 4728 / CC1/2: 0.842 / Rsym value: 0.487 / % 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 / Resolution: 1.97→48.913 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.65
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1480 5 %Random selection
Rwork0.2105 ---
obs0.2123 29617 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→48.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 63 95 2960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072959
X-RAY DIFFRACTIONf_angle_d0.7844025
X-RAY DIFFRACTIONf_dihedral_angle_d17.6871747
X-RAY DIFFRACTIONf_chiral_restr0.045424
X-RAY DIFFRACTIONf_plane_restr0.004555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9669-2.03040.32781300.28322479X-RAY DIFFRACTION97
2.0304-2.10290.30311360.2612581X-RAY DIFFRACTION100
2.1029-2.18710.31091340.24172551X-RAY DIFFRACTION100
2.1871-2.28670.26231350.22452556X-RAY DIFFRACTION100
2.2867-2.40720.25131340.222545X-RAY DIFFRACTION99
2.4072-2.55810.28981330.22542536X-RAY DIFFRACTION100
2.5581-2.75550.27881350.23462554X-RAY DIFFRACTION100
2.7555-3.03280.28861350.23982581X-RAY DIFFRACTION100
3.0328-3.47160.2981340.22992547X-RAY DIFFRACTION99
3.4716-4.37340.1871360.18052583X-RAY DIFFRACTION100
4.3734-48.92820.20731380.17922624X-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)
10.1374-0.0033-0.10230.39340.32830.0645-0.1247-0.328-0.10240.49930.0187-0.03330.37760.1047-0.03810.5891-0.0338-0.03670.44070.12030.355317.7164-20.709820.2021
20.52920.38080.06990.7143-0.17610.1918-0.0424-0.3024-0.09890.8336-0.36030.20080.5833-0.17-0.46460.69990.12170.00020.28020.21360.231718.7044-18.77118.7587
30.2227-0.01650.31030.96880.09010.6393-0.0583-0.1579-0.22840.3692-0.0761-0.13220.37890.1521-0.00710.42820.03420.07190.26710.10850.339817.2483-24.92694.5692
41.24660.0674-0.55140.9266-0.04150.6186-0.0567-0.0185-0.0035-0.048-0.0506-0.01490.23420.0622-0.09150.28170.03420.04790.23860.06190.279412.0934-18.4573-6.3716
50.1370.0557-0.31030.3985-0.15520.2552-0.09510.4666-0.187-0.3123-0.09760.03130.2457-0.1213-0.00120.43230.06640.07850.33780.00660.319614.3206-26.6514-18.9035
60.9302-0.20120.16360.94510.0990.115-0.1256-0.3071-0.23690.29210.0157-0.2210.37180.3523-0.21310.39060.09470.08510.28530.15980.315920.7457-23.14019.4611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 160 )
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 252 )
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 297 )
6X-RAY DIFFRACTION6chain 'A' and (resid 298 through 350 )

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