[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleReversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions.
Journal, issue, pagesJ. Am. Chem. Soc., Vol. 143, Page 8454-8464, Year 2021
Publish dateOct 14, 2020 (structure data deposition date)
AuthorsCossar, P.J. / Wolter, M. / van Dijck, L. / Valenti, D. / Levy, L.M. / Ottmann, C. / Brunsveld, L.
External linksJ. Am. Chem. Soc. / PubMed:34047554
MethodsX-ray diffraction
Resolution1.081 - 1.9 Å
Structure data

PDB-7aog:
14-3-3 sigma in complex with Pin1 binding site pS72
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-7axn:
14-3-3 sigma in complex with Pin1 binding site pS72 and covalently bound TCF521-026
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7ayf:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound TCF521-110
Method: X-RAY DIFFRACTION / Resolution: 1.752 Å

PDB-7az1:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1013
Method: X-RAY DIFFRACTION / Resolution: 1.15 Å

PDB-7az2:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1014
Method: X-RAY DIFFRACTION / Resolution: 1.081 Å

PDB-7bdp:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1017
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7bdt:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1009
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7bdy:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound PC2068B
Method: X-RAY DIFFRACTION / Resolution: 1.801 Å

PDB-7bfw:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound PC2068A
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7bg3:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound PC2046
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7bgq:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1019
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7bgr:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1016
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7bgv:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1012
Method: X-RAY DIFFRACTION / Resolution: 1.683 Å

PDB-7bgw:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1011
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7nif:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound TCF521-011
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-7nig:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1008
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7nix:
14-3-3 sigma with AS160 binding site pT642
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7nj6:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1005
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7nj8:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1007
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7nja:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1006
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7nqp:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound LvD1009
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-7nrk:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1002F1
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7nrl:
14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1032
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7nsv:
14-3-3 sigma with p65 (RelA) binding site pS45 and covalently bound PC2046
Method: X-RAY DIFFRACTION / Resolution: 1.33 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-HOH:
WATER / Water

ChemComp-S6B:
3-chloranyl-4-imidazol-1-yl-benzaldehyde

ChemComp-S9E:
6-(2-bromanylimidazol-1-yl)pyridine-3-carbaldehyde

ChemComp-SGH:
1-[4-methyl-3-(trifluoromethyl)phenyl]-2-phenyl-imidazole

ChemComp-SFW:
1-[4-methyl-2-(trifluoromethyl)phenyl]-2-phenyl-imidazole

ChemComp-TJB:
2-chloranyl-4-(2-phenylimidazol-1-yl)benzaldehyde

ChemComp-MG:
Unknown entry

ChemComp-TJ8:
2-bromanyl-4-(2-phenylimidazol-1-yl)benzaldehyde

ChemComp-TJK:
2-bromanyl-4-[2-(5-bromanyl-2-fluoranyl-phenyl)imidazol-1-yl]benzaldehyde

ChemComp-TKH:
[4-[2-[2,4-bis(fluoranyl)phenyl]imidazol-1-yl]-2-bromanyl-phenyl]methanol

ChemComp-TKK:
1-(3-bromanyl-4-methyl-phenyl)-2-(2-bromophenyl)imidazole

ChemComp-TL8:
2-methoxy-4-(2-phenylimidazol-1-yl)benzaldehyde

ChemComp-TQK:
2-methyl-4-(2-phenylimidazol-1-yl)benzaldehyde

ChemComp-TLK:
3-methoxy-4-(2-phenylimidazol-1-yl)benzaldehyde

ChemComp-TLQ:
4-(2-phenylimidazol-1-yl)naphthalene-1-carbaldehyde

ChemComp-NA:
Unknown entry

ChemComp-P5N:
1-(4-methylphenyl)imidazole

ChemComp-UFH:
2-bromanyl-4-imidazol-1-yl-benzaldehyde

ChemComp-NHE:
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / pH buffer*YM / CHES (buffer)

ChemComp-UG5:
4-[4-(trifluoromethyl)imidazol-1-yl]benzaldehyde

ChemComp-JFS:
[4-(1H-benzimidazol-1-yl)phenyl]methanol

ChemComp-UG2:
[4-(2-phenylimidazol-1-yl)phenyl]methanol

ChemComp-UPQ:
4-(4-methylimidazol-1-yl)benzaldehyde

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-UPK:
2-(hydroxymethyl)-5-(2-phenylimidazol-1-yl)phenol

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-UQN:
1-(3-bromanyl-4-methyl-phenyl)-2-(2-bromophenyl)imidazole

Source
  • homo sapiens (human)
KeywordsPEPTIDE BINDING PROTEIN / 1433 / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / TBC1 domain family member 4 / peptide-protein complex / benzaldehyde / covalent fragment / p65 / imine formation

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more