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- PDB-3ugd: Structural and functional characterization of an anesthetic bindi... -

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Basic information

Entry
Database: PDB / ID: 3ugd
TitleStructural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C delta
ComponentsProtein kinase C delta type
KeywordsMETAL BINDING PROTEIN / Proteine kinase C delta / PHOSPHOTRANSFERASE / Anesthetic binding site
Function / homology
Function and homology information


DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / VEGFR2 mediated cell proliferation / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / Effects of PIP2 hydrolysis / regulation of ceramide biosynthetic process / Interferon gamma signaling / HuR (ELAVL1) binds and stabilizes mRNA ...DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / VEGFR2 mediated cell proliferation / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / Effects of PIP2 hydrolysis / regulation of ceramide biosynthetic process / Interferon gamma signaling / HuR (ELAVL1) binds and stabilizes mRNA / Calmodulin induced events / protein kinase C signaling / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / negative regulation of filopodium assembly / endolysosome / positive regulation of ceramide biosynthetic process / Role of phospholipids in phagocytosis / termination of signal transduction / cellular response to hydroperoxide / protein kinase C / CLEC7A (Dectin-1) signaling / RHO GTPases Activate NADPH Oxidases / negative regulation of glial cell apoptotic process / negative regulation of actin filament polymerization / neutrophil activation / negative regulation of platelet aggregation / immunoglobulin mediated immune response / B cell proliferation / cellular response to angiotensin / insulin receptor substrate binding / positive regulation of superoxide anion generation / negative regulation of MAPK cascade / Neutrophil degranulation / negative regulation of insulin receptor signaling pathway / post-translational protein modification / positive regulation of apoptotic signaling pathway / cell chemotaxis / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / enzyme activator activity / peptidyl-serine phosphorylation / positive regulation of protein import into nucleus / negative regulation of inflammatory response / nuclear matrix / cellular response to hydrogen peroxide / cellular response to UV / cell-cell junction / cellular senescence / defense response to bacterium / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / protein kinase binding / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / zinc ion binding / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. ...Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / 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 / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protein kinase C delta type
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsShanmugasundararaj, S. / Stehle, T. / Miller, K.W.
Citation
Journal: Biophys.J. / Year: 2012
Title: Structural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C delta
Authors: Shanmugasundararaj, S. / Das, J. / Sandberg, W.S. / Zhou, X. / Wang, D. / Messing, R.O. / Bruzik, K.S. / Stehle, T. / Miller, K.W.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal structure of the cys2 activator-binding domain of protein kinase C delta in complex with phorbol ester.
Authors: Zhang, G. / Kazanietz, M.G. / Blumberg, P.M. / Hurley, J.H.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C delta type
B: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,65914
Polymers14,7032
Non-polymers95612
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-33 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.946, 32.504, 49.677
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein kinase C delta type / nPKC-delta


Mass: 7351.527 Da / Num. of mol.: 2 / Fragment: C1B Subdomain of PKC delta, UNP residues 231-280 / Mutation: Y236H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcd, Pkcd / Production host: Escherichia coli (E. coli) / References: UniProt: P28867, protein kinase C
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 3350 in 0.2 M ammonium sulfate and 25 mM HEPES pH 7.2. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2004
RadiationMonochromator: SI(111) CHANNEL CULT MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→10 Å / Num. all: 24847 / Num. obs: 23591 / % possible obs: 99.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PTQ

1ptq


Resolution: 1.45→9.956 Å / SU ML: 0.16 / σ(F): 0.02 / Phase error: 19.66 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 1987 8.81 %10%
Rwork0.1727 ---
all0.1766 24847 --
obs0.1766 22542 90.02 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.493 Å2 / ksol: 0.549 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7679 Å20 Å2-0.7007 Å2
2---1.4185 Å2-0 Å2
3---0.6505 Å2
Refinement stepCycle: LAST / Resolution: 1.45→9.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 42 185 1245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061070
X-RAY DIFFRACTIONf_angle_d1.1231432
X-RAY DIFFRACTIONf_dihedral_angle_d13.875380
X-RAY DIFFRACTIONf_chiral_restr0.072146
X-RAY DIFFRACTIONf_plane_restr0.004178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48620.25761350.21511296X-RAY DIFFRACTION80
1.4862-1.52620.23251370.18841323X-RAY DIFFRACTION83
1.5262-1.57090.23751190.17221412X-RAY DIFFRACTION86
1.5709-1.62140.21591400.16181437X-RAY DIFFRACTION89
1.6214-1.67910.19211500.15381461X-RAY DIFFRACTION91
1.6791-1.7460.20841350.1471489X-RAY DIFFRACTION91
1.746-1.8250.19431360.15061381X-RAY DIFFRACTION85
1.825-1.92060.22061340.15281375X-RAY DIFFRACTION85
1.9206-2.040.18011420.1611565X-RAY DIFFRACTION96
2.04-2.19590.21911640.17741619X-RAY DIFFRACTION99
2.1959-2.4140.23051500.1611537X-RAY DIFFRACTION95
2.414-2.75680.23541440.18351521X-RAY DIFFRACTION91
2.7568-3.44920.22161410.18891538X-RAY DIFFRACTION93
3.4492-9.95610.21671600.17881601X-RAY DIFFRACTION95

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