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

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Basic information

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


DAG and IP3 signaling / positive regulation of phospholipid scramblase activity / positive regulation of glucosylceramide catabolic process / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / VEGFR2 mediated cell proliferation / regulation of ceramide biosynthetic process / Interferon gamma signaling / Effects of PIP2 hydrolysis ...DAG and IP3 signaling / positive regulation of phospholipid scramblase activity / positive regulation of glucosylceramide catabolic process / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / VEGFR2 mediated cell proliferation / regulation of ceramide biosynthetic process / Interferon gamma signaling / Effects of PIP2 hydrolysis / HuR (ELAVL1) binds and stabilizes mRNA / phospholipase C/protein kinase C signal transduction / TIR domain binding / Calmodulin induced events / protein kinase C signaling / calcium,diacylglycerol-dependent serine/threonine kinase activity / negative regulation of filopodium assembly / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / endolysosome / positive regulation of ceramide biosynthetic process / Role of phospholipids in phagocytosis / diacylglycerol-dependent serine/threonine kinase activity / termination of signal transduction / cellular response to hydroperoxide / protein kinase C / negative regulation of actin filament polymerization / RHO GTPases Activate NADPH Oxidases / collagen metabolic process / negative regulation of glial cell apoptotic process / CLEC7A (Dectin-1) signaling / neutrophil activation / regulation of phosphorylation / D-aspartate import across plasma membrane / negative regulation of platelet aggregation / B cell proliferation / immunoglobulin mediated immune response / peptidyl-threonine phosphorylation / positive regulation of MAP kinase activity / cellular response to angiotensin / insulin receptor substrate binding / protein tyrosine kinase activator activity / postsynaptic cytosol / negative regulation of MAPK cascade / positive regulation of superoxide anion generation / negative regulation of insulin receptor signaling pathway / positive regulation of D-glucose import across plasma membrane / Neutrophil degranulation / positive regulation of apoptotic signaling pathway / post-translational protein modification / positive regulation of DNA repair / regulation of actin cytoskeleton organization / protein serine/threonine kinase binding / non-specific protein-tyrosine kinase / cell chemotaxis / positive regulation of protein import into nucleus / non-membrane spanning protein tyrosine kinase activity / negative regulation of inflammatory response / peptidyl-serine phosphorylation / cellular senescence / cellular response to hydrogen peroxide / enzyme activator activity / nuclear matrix / cell-cell junction / cellular response to UV / protein autophosphorylation / response to oxidative stress / cellular response to oxidative stress / positive regulation of MAPK cascade / protein kinase activity / protein phosphorylation / defense response to bacterium / intracellular signal transduction / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / endoplasmic reticulum / mitochondrion / zinc ion binding / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
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: 1.301 Å
AuthorsShanmugasundararaj, S. / Stehle, T. / Miller, K.W.
CitationJournal: Biophys.J. / Year: 2012
Title: Structural and Functional Characterization of an Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase Cdelta
Authors: Shanmugasundararaj, S. / Das, J. / Sandberg, W.S. / Zhou, X. / Wang, D. / Messing, R.O. / Bruzik, K.S. / Stehle, T. / Miller, K.W.
History
DepositionOct 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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_seq_id / _struct_conn.ptnr2_label_asym_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)15,39510
Polymers14,7532
Non-polymers6428
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-20 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.598, 32.475, 49.965
Angle α, β, γ (deg.)90.00, 94.10, 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: 7376.554 Da / Num. of mol.: 2 / Fragment: C1B Subdomain of PKC delta, UNP residues 231-280
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A11
SYNCHROTRONAPS 8-BM20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 27, 2004
ADSC QUANTUM 2102CCDApr 22, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111) CHANNEL CULT MONOCHROMATSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
ReflectionResolution: 1.3→30 Å / Num. all: 42420 / Num. obs: 34350 / % possible obs: 95.87 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Rsym value: 0.08 / Net I/σ(I): 15.34
Reflection shell
Resolution (Å)Diffraction-ID
1.35-1.421,2
1.42-1.511,2
1.51-1.631,2
1.63-1.791,2
1.79-2.051,2
2.05-2.591,2
2.59-501,2

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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: 1.301→9.983 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 13.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1582 1921 5.81 %
Rwork0.1424 --
obs0.1433 33058 95.87 %
all-42420 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.619 Å2 / ksol: 0.511 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6885 Å2-0 Å20.9309 Å2
2---2.4434 Å20 Å2
3---0.7549 Å2
Refinement stepCycle: LAST / Resolution: 1.301→9.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 24 222 1270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071070
X-RAY DIFFRACTIONf_angle_d1.2171440
X-RAY DIFFRACTIONf_dihedral_angle_d13.468388
X-RAY DIFFRACTIONf_chiral_restr0.085148
X-RAY DIFFRACTIONf_plane_restr0.005182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.301-1.33340.25571250.21172014X-RAY DIFFRACTION88
1.3334-1.36940.22061240.17612104X-RAY DIFFRACTION91
1.3694-1.40950.19481490.15382096X-RAY DIFFRACTION92
1.4095-1.45490.15861320.13672170X-RAY DIFFRACTION94
1.4549-1.50670.15711340.1122182X-RAY DIFFRACTION95
1.5067-1.56680.12941380.10942225X-RAY DIFFRACTION96
1.5668-1.63790.12741290.10612242X-RAY DIFFRACTION97
1.6379-1.72380.13771450.10462263X-RAY DIFFRACTION98
1.7238-1.83120.12821350.1112249X-RAY DIFFRACTION97
1.8312-1.97160.14281370.12952234X-RAY DIFFRACTION97
1.9716-2.16810.1531480.13732352X-RAY DIFFRACTION100
2.1681-2.47770.17281440.1482297X-RAY DIFFRACTION99
2.4777-3.10590.16851380.16352315X-RAY DIFFRACTION99
3.1059-9.98370.15491430.16062394X-RAY DIFFRACTION99

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