[English] 日本語
Yorodumi
- PDB-8fp3: PKCeta kinase domain in complex with compound 11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fp3
TitlePKCeta kinase domain in complex with compound 11
ComponentsProtein kinase C eta type
KeywordsTRANSFERASE/INHIBITOR / HPK1 / Structure based drug design / cancer / kinase / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / positive regulation of B cell receptor signaling pathway / protein kinase C signaling / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / positive regulation of macrophage derived foam cell differentiation / positive regulation of keratinocyte differentiation / regulation of bicellular tight junction assembly ...diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / positive regulation of B cell receptor signaling pathway / protein kinase C signaling / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / positive regulation of macrophage derived foam cell differentiation / positive regulation of keratinocyte differentiation / regulation of bicellular tight junction assembly / positive regulation of glial cell proliferation / positive regulation of protein localization to plasma membrane / small GTPase binding / G alpha (z) signalling events / cell-cell junction / positive regulation of NF-kappaB transcription factor activity / cell differentiation / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / enzyme binding / signal transduction / extracellular exosome / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein kinase C, eta / Novel protein kinase C eta, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) ...Protein kinase C, eta / Novel protein kinase C eta, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / 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
Similarity search - Domain/homology
Chem-Y3I / Protein kinase C eta type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJohnson, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Design and Synthesis of Functionally Active 5-Amino-6-Aryl Pyrrolopyrimidine Inhibitors of Hematopoietic Progenitor Kinase 1.
Authors: Gallego, R.A. / Bernier, L. / Chen, H. / Cho-Schultz, S. / Chung, L. / Collins, M. / Del Bel, M. / Elleraas, J. / Costa Jones, C. / Cronin, C.N. / Edwards, M. / Fang, X. / Fisher, T. / He, M. ...Authors: Gallego, R.A. / Bernier, L. / Chen, H. / Cho-Schultz, S. / Chung, L. / Collins, M. / Del Bel, M. / Elleraas, J. / Costa Jones, C. / Cronin, C.N. / Edwards, M. / Fang, X. / Fisher, T. / He, M. / Hoffman, J. / Huo, R. / Jalaie, M. / Johnson, E. / Johnson, T.W. / Kania, R.S. / Kraus, M. / Lafontaine, J. / Le, P. / Liu, T. / Maestre, M. / Matthews, J. / McTigue, M. / Miller, N. / Mu, Q. / Qin, X. / Ren, S. / Richardson, P. / Rohner, A. / Sach, N. / Shao, L. / Smith, G. / Su, R. / Sun, B. / Timofeevski, S. / Tran, P. / Wang, S. / Wang, W. / Zhou, R. / Zhu, J. / Nair, S.K.
History
DepositionJan 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein kinase C eta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9302
Polymers40,5631
Non-polymers3671
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.239, 77.736, 95.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein kinase C eta type / PKC-L / nPKC-eta


Mass: 40563.035 Da / Num. of mol.: 1 / Fragment: residues 333-683 / Mutation: S675E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCH, PKCL, PRKCL / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24723, protein kinase C
#2: Chemical ChemComp-Y3I / (3P)-3-{4-[(3R,5S)-3-amino-5-methylpiperidin-1-yl]-6-chloro-7H-pyrrolo[2,3-d]pyrimidin-5-yl}benzonitrile


Mass: 366.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19ClN6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 286.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Well Ingredients: Precipitant: 21.0 %w/v (10.5 uL of stock 50.0 %w/v) PEG 3350 Salt: 0.7 M (2.1875 uL of stock 8.0 M) lithium nitrate Buffer: 0.1 M (2.5 uL of stock 1.0 M) MES (pH 6.00) ...Details: Well Ingredients: Precipitant: 21.0 %w/v (10.5 uL of stock 50.0 %w/v) PEG 3350 Salt: 0.7 M (2.1875 uL of stock 8.0 M) lithium nitrate Buffer: 0.1 M (2.5 uL of stock 1.0 M) MES (pH 6.00) Organic (non-volatile): 7.0 % w/v (2.1875 uL of stock 80.0 % w/v) Glycerol [Protien] = 12 mg/ml
Temp details: 13 degrees C.

-
Data collection

DiffractionMean temperature: 87.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→77.74 Å / Num. obs: 18820 / % possible obs: 98.2 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.044 / Net I/σ(I): 12.6
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 6.8 % / Num. unique obs: 2565 / CC1/2: 0.794 / % possible all: 99.2

-
Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2559 -5 %
Rwork0.1983 --
obs-17907 100 %
Refinement stepCycle: LAST / Resolution: 2.3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 26 172 2889

+
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://pdbjlvh1.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