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- PDB-1cdk: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT (E.C.2.7.1.37) (P... -

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Entry
Database: PDB / ID: 1cdk
TitleCAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT (E.C.2.7.1.37) (PROTEIN KINASE A) COMPLEXED WITH PROTEIN KINASE INHIBITOR PEPTIDE FRAGMENT 5-24 (PKI(5-24) ISOELECTRIC VARIANT CA) AND MN2+ ADENYLYL IMIDODIPHOSPHATE (MNAMP-PNP) AT PH 5.6 AND 7C AND 4C
Components
  • CAMP-DEPENDENT PROTEIN KINASE
  • PROTEIN KINASE INHIBITOR
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / COMPLEX (TRANSFERASE-INHIBITOR) / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of meiotic cell cycle process involved in oocyte maturation / 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 ...negative regulation of meiotic cell cycle process involved in oocyte maturation / 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 / RET signaling / AURKA Activation by TPX2 / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / negative regulation of cAMP-dependent protein kinase activity / VEGFA-VEGFR2 Pathway / negative regulation of cAMP/PKA signal transduction / PKA activation / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / germinal vesicle / 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 / negative regulation of protein import into nucleus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / molecular function inhibitor activity / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / molecular adaptor activity / protein kinase activity / protein phosphorylation / protein domain specific binding / 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 / 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. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / MYRISTIC ACID / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBossemeyer, D. / Engh, R.A. / Kinzel, V. / Ponstingl, H. / Huber, R.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: 2.2 Angstrom Refined Crystal Structure of the Catalytic Subunit of cAMP-Dependent Protein Kinase Complexed with Mnatp and a Peptide Inhibitor
Authors: Zheng, J. / Trafny, E.A. / Knighton, D.R. / Xuong, N.-H. / Taylor, S.S. / Ten Eyck, L.F. / Sowadski, J.M.
#2: Journal: Protein Sci. / Year: 1993
Title: Crystal Structures of the Myristylated Catalytic Subunit Ofcamp-Dependent Kinase Reveal Open and Closed Conformation
Authors: Zheng, J. / Knighton, D.R. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. / Ten Eyck, L.F.
#3: Journal: Science / Year: 1991
Title: Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate Dependent-Protein Kinase
Authors: Knighton, D.R. / Zheng, J.H. / Ten Eyck, L.F. / Ashford, V.A. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M.
#4: Journal: Science / Year: 1991
Title: Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of a Cyclic Adenosine Monophosphate-Dependent Protein Kinase
Authors: Knighton, D.R. / Zheng, J. / Ten Eyck, L.F. / Xoung, N.-H. / Taylor, S.S. / Sowadski, J.M.
#5: Journal: Nature / Year: 1991
Title: Regulation by Phosphorylation of Reversible Association of a Myristoylated Protein Kinase C Substrate with the Plasma Membrane
Authors: Thelen, M. / Rosen, A. / Nairn, A.C. / Aderem, A.
#6: Journal: FEBS Lett. / Year: 1989
Title: A Sequence Variant in the N-Terminal Region of the Catalytic Subunit of the cAMP-Dependent Protein Kinase
Authors: Hotz, A. / Konig, N. / Kretschmer, J. / Maier, G. / Ponstingl, H. / Kinzel, V.
#7: Journal: J.Biol.Chem. / Year: 1988
Title: Characterization of Genomic Clones Coding for the C-Alpha and C-Beta Subunits of Mouse Camp Dependent Protein Kinase
Authors: Chrivia, J.C. / Uhler, M.D. / Mcknight, G.S.
History
DepositionJul 4, 1994Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2012Group: Source and taxonomy
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 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
I: PROTEIN KINASE INHIBITOR
B: CAMP-DEPENDENT PROTEIN KINASE
J: PROTEIN KINASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,39312
Polymers85,7044
Non-polymers1,6898
Water5,621312
1
A: CAMP-DEPENDENT PROTEIN KINASE
I: PROTEIN KINASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6966
Polymers42,8522
Non-polymers8444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-18 kcal/mol
Surface area15940 Å2
MethodPISA
2
B: CAMP-DEPENDENT PROTEIN KINASE
J: PROTEIN KINASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6966
Polymers42,8522
Non-polymers8444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-17 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.610, 80.600, 110.100
Angle α, β, γ (deg.)90.00, 88.59, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9997, 0.0125, 0.0222), (-0.0121, 0.9998, -0.0168), (-0.0222, 0.0165, 0.9996)
Vector: 53.2182, 28.0206, 0.6126)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 8 .. B 317 A 8 .. A 317 0.265 M1 B 322 .. B 350 A 322 .. A 350 0.347

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABIJ

#1: Protein CAMP-DEPENDENT PROTEIN KINASE / PROTEIN KINASE A


Mass: 40625.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: HEART / Tissue: HEART ISOFORM CA
References: UniProt: P00517, UniProt: P36887*PLUS, cAMP-dependent protein kinase
#2: Protein/peptide PROTEIN KINASE INHIBITOR / PKI(5-24)


Mass: 2226.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925, UniProt: P61926*PLUS

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Non-polymers , 4 types, 320 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 280 K / pH: 5.6 / Details: pH 5.6, temperature 280K
Crystal grow
*PLUS
Method: vapor diffusion

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 58447
Reflection
*PLUS
% possible obs: 83.5 % / Num. measured all: 103697 / Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→5 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.197 -
obs0.197 49638
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5971 0 78 312 6361
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
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_deg2.96
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

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