[English] 日本語
Yorodumi
- PDB-3uey: Structural and functional characterization of an anesthetic bindi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uey
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 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: 1.301 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 31, 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,55312
Polymers14,7212
Non-polymers83110
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-34 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.876, 32.522, 49.816
Angle α, β, γ (deg.)90.00, 94.02, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 7360.555 Da / Num. of mol.: 2 / Fragment: C1B Subdomain of PKC delta, UNP residues 231-280 / Mutation: Y236F
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.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.93 %
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

-
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 MONOCHROMAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→10 Å / Num. all: 33077 / Num. obs: 31416 / % possible obs: 95.47 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2

-
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→9.986 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 1837 6.01 %10%
Rwork0.188 ---
all0.1904 33077 --
obs0.1904 30558 88.23 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.885 Å2 / ksol: 0.51 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1102 Å2-0 Å2-0.3982 Å2
2---0.7296 Å2-0 Å2
3---0.6195 Å2
Refinement stepCycle: LAST / Resolution: 1.301→9.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 34 230 1286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071068
X-RAY DIFFRACTIONf_angle_d1.1381434
X-RAY DIFFRACTIONf_dihedral_angle_d13.814380
X-RAY DIFFRACTIONf_chiral_restr0.076146
X-RAY DIFFRACTIONf_plane_restr0.005180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3011-1.33620.291990.25891526X-RAY DIFFRACTION62
1.3362-1.37540.29441280.25691810X-RAY DIFFRACTION74
1.3754-1.41970.28861250.22292000X-RAY DIFFRACTION80
1.4197-1.47030.2551360.18872119X-RAY DIFFRACTION85
1.4703-1.52890.19471510.16732225X-RAY DIFFRACTION90
1.5289-1.59830.20021470.152294X-RAY DIFFRACTION92
1.5983-1.68210.20961420.14242342X-RAY DIFFRACTION94
1.6821-1.7870.19631420.14782322X-RAY DIFFRACTION93
1.787-1.9240.20621430.15842255X-RAY DIFFRACTION90
1.924-2.1160.20961580.17522469X-RAY DIFFRACTION98
2.116-2.41840.21411560.18252456X-RAY DIFFRACTION98
2.4184-3.03270.23911560.21082414X-RAY DIFFRACTION95
3.0327-9.98610.24711540.20682489X-RAY DIFFRACTION96

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more