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- PDB-1stc: CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1stc
TitleCAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT IN COMPLEX WITH STAUROSPORINE
Components
  • CAMP-DEPENDENT PROTEIN KINASE
  • PROTEIN KINASE INHIBITOR
KeywordsCOMPLEX (TRANSFERASE/INHIBITOR) / PROTEIN KINASE / STAUROSPORINE / CAMP / PHOSPHORYLATION / COMPLEX (TRANSFERASE-INHIBITOR) / SERINE/THREONINE-PROTEIN KINASE / COMPLEX (TRANSFERASE-INHIBITOR) complex
Function / homology
Function and homology information


CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / negative regulation of cAMP-dependent protein kinase activity / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of protein import into nucleus / Vasopressin regulates renal water homeostasis via Aquaporins / molecular function inhibitor activity / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / protein kinase A signaling / regulation of G2/M transition of mitotic cell cycle / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / molecular adaptor activity / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / 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. / 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
STAUROSPORINE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPrade, L. / Engh, R.A. / Girod, A. / Kinzel, V. / Huber, R. / Bossemeyer, D.
Citation
Journal: Structure / Year: 1997
Title: Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential.
Authors: Prade, L. / Engh, R.A. / Girod, A. / Kinzel, V. / Huber, R. / Bossemeyer, D.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Crystal Structures of Catalytic Subunit of Camp-Dependent Protein Kinase in Complex with Isoquinolinesulfonyl Protein Kinase Inhibitors H7, H8, and H89. Structural Implications for Selectivity
Authors: Engh, R.A. / Girod, A. / Kinzel, V. / Huber, R. / Bossemeyer, D.
#2: Journal: Embo J. / Year: 1993
Title: Phosphotransferase and Substrate Binding Mechanism of the Camp-Dependent Protein Kinase Catalytic Subunit from Porcine Heart as Deduced from the 2.0 A Structure of the Complex with Mn2+ ...Title: Phosphotransferase and Substrate Binding Mechanism of the Camp-Dependent Protein Kinase Catalytic Subunit from Porcine Heart as Deduced from the 2.0 A Structure of the Complex with Mn2+ Adenylyl Imidodiphosphate and Inhibitor Peptide Pki(5-24)
Authors: Bossemeyer, D. / Engh, R.A. / Kinzel, V. / Ponstingl, H. / Huber, R.
#3: Journal: J.Antibiot. / Year: 1977
Title: A New Alkaloid Am-2282 of Streptomyces Origin. Taxonomy, Fermentation, Isolation and Preliminary Characterization
Authors: Omura, S. / Iwai, Y. / Hirano, A. / Nakagawa, A. / Awaya, J. / Tsuchya, H. / Takahashi, Y. / Masuma, R.
History
DepositionOct 10, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
E: CAMP-DEPENDENT PROTEIN KINASE
I: PROTEIN KINASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4793
Polymers43,0132
Non-polymers4671
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.990, 72.820, 76.630
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 / CAPK / PROTEIN KINASE A / PKA C-ALPHA


Mass: 40786.395 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line: BL21 / Organ: HEART / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYS / References: UniProt: P00517, EC: 2.7.1.37
#2: Protein/peptide PROTEIN KINASE INHIBITOR / PKI / PKI-ALPHA


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: INHIBITORY DOMAIN
Source method: isolated from a genetically manipulated source
References: UniProt: P04541, UniProt: P61926*PLUS
#3: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 6.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mMMES-Bis-Tris1drop
21.5 mMoctanoyl-N-methylglucamide1drop
315 %methanol1reservoir
9o1

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→32 Å / Num. obs: 16993 / % possible obs: 92.2 % / Redundancy: 3.8 % / Rsym value: 0.073
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 3 / % possible all: 92.3
Reflection
*PLUS
Num. measured all: 64256 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 92.3 % / Rmerge(I) obs: 0.246

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CDK

1cdk


Resolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.33 -10 %
Rwork0.208 --
obs0.208 15467 92.2 %
Displacement parametersBiso mean: 34.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 43 142 3096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.547
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.38 Å / % reflection obs: 92.3 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.333
Solvent computation
*PLUS
Displacement parameters
*PLUS

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