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- PDB-5c6c: PKG II's Amino Terminal Cyclic Nucleotide Binding Domain (CNB-A) ... -

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Basic information

Entry
Database: PDB / ID: 5c6c
TitlePKG II's Amino Terminal Cyclic Nucleotide Binding Domain (CNB-A) in a complex with cAMP
ComponentscGMP-dependent protein kinase 2
KeywordsPROTEIN BINDING / Binding Sites / Cyclic AMP / Cyclic GMP / Cyclic GMP-Dependent Protein Kinase Type II / Mutagenesis / Site-Directed
Function / homology
Function and homology information


negative regulation of chloride transport / tetrahydrobiopterin metabolic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / positive regulation of chondrocyte differentiation / mitogen-activated protein kinase binding / cGMP effects / cGMP binding / positive regulation of protein localization / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation ...negative regulation of chloride transport / tetrahydrobiopterin metabolic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / positive regulation of chondrocyte differentiation / mitogen-activated protein kinase binding / cGMP effects / cGMP binding / positive regulation of protein localization / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / protein kinase A signaling / protein localization to plasma membrane / RAS processing / Ca2+ pathway / nuclear membrane / protein kinase activity / protein phosphorylation / apical plasma membrane / protein serine kinase activity / signal transduction / ATP binding / identical protein binding / cytosol
Similarity search - Function
cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / : / cGMP-dependent protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.05 Å
AuthorsCampbell, J.C. / Reger, A.S. / Huang, G.Y. / Sankaran, B. / Kim, J.J. / Kim, C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM090161 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II.
Authors: Campbell, J.C. / Kim, J.J. / Li, K.Y. / Huang, G.Y. / Reger, A.S. / Matsuda, S. / Sankaran, B. / Link, T.M. / Yuasa, K. / Ladbury, J.E. / Casteel, D.E. / Kim, C.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cGMP-dependent protein kinase 2
B: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,88818
Polymers33,1542
Non-polymers1,73416
Water1,910106
1
A: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,52210
Polymers16,5771
Non-polymers9459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3658
Polymers16,5771
Non-polymers7887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.710, 63.760, 99.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein cGMP-dependent protein kinase 2 / cGK2 / cGMP-dependent protein kinase II / cGKII


Mass: 16576.941 Da / Num. of mol.: 2 / Fragment: unp residues 137-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG2, PRKGR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13237, cGMP-dependent protein kinase

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Non-polymers , 7 types, 122 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 44.98 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 200 mM calcium chloride, 200 mM cadmium chloride, 200 mM cobalt (II) chloride, 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→39.233 Å / Num. obs: 18656 / % possible obs: 96.7 % / Redundancy: 6.6 % / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→39.233 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 1877 10.06 %
Rwork0.1862 --
obs0.1919 18656 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→39.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 61 106 1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071865
X-RAY DIFFRACTIONf_angle_d1.0462538
X-RAY DIFFRACTIONf_dihedral_angle_d13.234656
X-RAY DIFFRACTIONf_chiral_restr0.037296
X-RAY DIFFRACTIONf_plane_restr0.004314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10540.28581300.22321156X-RAY DIFFRACTION89
2.1054-2.16740.2991350.20391179X-RAY DIFFRACTION92
2.1674-2.23730.25731380.20671233X-RAY DIFFRACTION93
2.2373-2.31730.2761440.20241269X-RAY DIFFRACTION96
2.3173-2.41010.25271400.18181241X-RAY DIFFRACTION95
2.4101-2.51970.26681430.17781276X-RAY DIFFRACTION97
2.5197-2.65250.27361440.18681296X-RAY DIFFRACTION98
2.6525-2.81870.25081450.19241316X-RAY DIFFRACTION99
2.8187-3.03620.24491470.18671311X-RAY DIFFRACTION99
3.0362-3.34160.26061490.19411354X-RAY DIFFRACTION100
3.3416-3.82480.2441490.17691331X-RAY DIFFRACTION100
3.8248-4.81750.20251520.15561367X-RAY DIFFRACTION100
4.8175-39.23980.21891610.20351450X-RAY DIFFRACTION100

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