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- PDB-4ujb: Protein Kinase A in complex with an Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4ujb
TitleProtein Kinase A in complex with an Inhibitor
Components
  • CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
  • PEPTIDE
KeywordsTRANSFERASE
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of cardiac muscle contraction / regulation of cardiac conduction / sperm flagellum / regulation of macroautophagy / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of gluconeogenesis / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / protein kinase A signaling / Mitochondrial protein degradation / calcium channel complex / Anchoring of the basal body to the plasma membrane / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / Regulation of insulin secretion / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / Factors involved in megakaryocyte development and platelet production / cellular response to heat / manganese ion binding / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle
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
Chem-8BQ / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsAlam, 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 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection / Experimental preparation
Category: atom_site / exptl_crystal_grow
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _exptl_crystal_grow.method
Revision 2.1Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
B: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6895
Polymers43,1152
Non-polymers5743
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-5.9 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.620, 75.371, 80.349
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 / PKA


Mass: 40888.547 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 1-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein/peptide PEPTIDE


Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61925*PLUS
#3: Chemical ChemComp-8BQ / 7-[(3S,4R)-4-(3-fluorophenyl)carbonylpyrrolidin-3-yl]-3H-quinazolin-4-one


Mass: 337.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16FN3O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNA (37A): NA

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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: 2.56 Å3/Da / Density % sol: 52.03 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10MG/ML PROTEIN, 25MM BISTRIS/MES PH6.9, 50MM KCL, 1.5MM OCTANOYL-N-METHYLGLUCAMIDE, 1MM PROTEIN KINASE INHIBITOR PEPTIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorDate: Oct 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→43.83 Å / Num. obs: 32724 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 23.39 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.83
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.94 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VQH

3vqh


Resolution: 1.949→43.83 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 18.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 1637 5 %
Rwork0.1546 --
obs0.1564 32721 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.949→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 41 420 3460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073125
X-RAY DIFFRACTIONf_angle_d0.944226
X-RAY DIFFRACTIONf_dihedral_angle_d14.2231152
X-RAY DIFFRACTIONf_chiral_restr0.04441
X-RAY DIFFRACTIONf_plane_restr0.005536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9485-2.00590.28321340.24152529X-RAY DIFFRACTION98
2.0059-2.07060.28791330.21482539X-RAY DIFFRACTION100
2.0706-2.14460.2591350.20162554X-RAY DIFFRACTION100
2.1446-2.23050.23061350.18382568X-RAY DIFFRACTION100
2.2305-2.3320.21441340.16632552X-RAY DIFFRACTION100
2.332-2.45490.21211360.15462580X-RAY DIFFRACTION100
2.4549-2.60870.18331360.15452583X-RAY DIFFRACTION100
2.6087-2.81010.18271360.16172581X-RAY DIFFRACTION100
2.8101-3.09280.19311370.15112610X-RAY DIFFRACTION100
3.0928-3.54020.18731360.1432592X-RAY DIFFRACTION100
3.5402-4.45960.14811400.12442654X-RAY DIFFRACTION100
4.4596-43.84080.1581450.14052742X-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)
10.5023-0.1648-0.22110.4339-0.42210.7329-0.00480.0248-0.0962-0.1468-0.01180.23150.1549-0.35080.03780.1487-0.0211-0.05560.248-0.01020.2357-36.51425.7599-9.9656
20.147-0.02480.0410.0973-0.18440.3488-0.06680.06070.36520.0940.10380.0938-0.2102-0.1872-0.00680.11420.01850.01730.1923-0.00630.2329-30.317419.62010.0621
30.3435-0.26660.08860.61540.11740.8-0.0018-0.05420.05220.00040.00490.13040.0279-0.175900.12170.0048-0.00220.1829-0.0180.1825-29.51938.8055-2.1238
40.3705-0.11780.16220.5399-0.26060.7698-0.01410.0144-0.1034-0.0819-0.020.02650.3013-0.056-00.1638-0.01390.0090.14-0.01420.1234-24.8701-3.5774-4.5737
50.20510.2531-0.48871.2744-0.47191.2116-0.0083-0.0524-0.2903-0.1501-0.1318-0.30670.58070.366-0.10750.3330.05920.00550.17560.03370.2069-14.4968-13.1863.6927
60.73630.1580.10950.1874-0.31110.76330.02390.0727-0.3344-0.05210.00550.15850.5639-0.16230.22140.3544-0.12090.01490.1808-0.01880.2214-32.1761-13.998-3.1127
70.5489-0.5235-0.17570.8563-0.09670.6763-0.0555-0.09060.11220.10290.0594-0.0496-0.281-0.0465-0.02910.17410.0122-0.0210.1596-0.01810.1875-27.034219.8481.9135
80.0055-0.00320.01230.0432-0.00420.02520.040.0595-0.0517-0.0288-0.12330.22450.14390.3457-0.00020.19990.01770.01380.2229-0.00770.1587-12.8889-8.269416.1186
90.13820.00920.10750.16450.05420.0979-0.1373-0.18580.15060.03250.032-0.1087-0.09330.0817-0.01390.1844-0.0078-0.00460.1450.00850.1799-13.67563.52164.4028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 54 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 55 THROUGH 81 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 82 THROUGH 139 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 140 THROUGH 233 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 234 THROUGH 272 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 273 THROUGH 316 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 317 THROUGH 350 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 5 THROUGH 11 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 12 THROUGH 24 )

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