[English] 日本語
Yorodumi
- PDB-1bfz: BOUND CONFORMATION OF N-TERMINAL CLEAVAGE PRODUCT PEPTIDE MIMIC (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bfz
TitleBOUND CONFORMATION OF N-TERMINAL CLEAVAGE PRODUCT PEPTIDE MIMIC (P1-P9 OF RELEASE SITE) WHILE BOUND TO HCMV PROTEASE AS DETERMINED BY TRANSFERRED NOESY EXPERIMENTS (P1-P5 SHOWN ONLY), NMR, 32 STRUCTURES
ComponentsHCMV PROTEASE R-SITE N-TERMINAL CLEAVAGE PRODUCT
KeywordsPEPTIDE / SUBSTRIATE CLEAVAGE / BOUND CONFORMATION / EXTENDED CONFORMATION / substrate-based competitive inhibitor design
MethodSOLUTION NMR / RESTRAINED SIMULATED ANNEALING
AuthorsLaplante, S.R. / Aubry, N. / Bonneau, P.R. / Cameron, D.R. / Lagace, L. / Massariol, M.-J. / Montpetit, H. / Ploufe, C. / Kawai, S.H. / Fulton, B.D. ...Laplante, S.R. / Aubry, N. / Bonneau, P.R. / Cameron, D.R. / Lagace, L. / Massariol, M.-J. / Montpetit, H. / Ploufe, C. / Kawai, S.H. / Fulton, B.D. / Chen, Z. / Ni, F.
CitationJournal: Biochemistry / Year: 1998
Title: Human cytomegalovirus protease complexes its substrate recognition sequences in an extended peptide conformation.
Authors: LaPlante, S.R. / Aubry, N. / Bonneau, P.R. / Cameron, D.R. / Lagace, L. / Massariol, M.J. / Montpetit, H. / Plouffe, C. / Kawai, S.H. / Fulton, B.D. / Chen, Z. / Ni, F.
History
DepositionMay 25, 1998Processing site: BNL
Revision 1.0May 25, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HCMV PROTEASE R-SITE N-TERMINAL CLEAVAGE PRODUCT


Theoretical massNumber of molelcules
Total (without water)5941
Polymers5941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 50POTENTIAL ENERGY, MINIMAL RESTRAINT VIOLATIONS
RepresentativeModel #4

-
Components

#1: Protein/peptide HCMV PROTEASE R-SITE N-TERMINAL CLEAVAGE PRODUCT


Mass: 593.693 Da / Num. of mol.: 1 / Fragment: TERESYVKA N-TERMINAL RESIDUES OF R-SITE PEPTIDE / Source method: obtained synthetically
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRNOESY
121NOESY
131TOCSY
NMR detailsText: TRANSFERRED NUCLEAR OVERHAUSER EFFECT SPECTROSCOPY 50, 150, 250 MS MIXING TIMES USED TO GENERATE RESTRAINTS

-
Sample preparation

DetailsContents: 0.5M NA2SO4, 50MM NACL, 1MM EDTA, 5MM DTT-D10 IN 10% D2O SPIKED WITH TSP-2,2,3,3-D4
Sample conditionspH: 7 / Temperature: 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX400BrukerAMX4004001
Bruker AMX500BrukerAMX5005002
Bruker DRX500BrukerDRX5006003
Bruker DMX600BrukerDMX6006004

-
Processing

NMR software
NameVersionDeveloperClassification
Discover95.5MSIrefinement
Discover95.5structure solution
RefinementMethod: RESTRAINED SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. CFF95 FORCEFIELD USED.
NMR ensembleConformer selection criteria: POTENTIAL ENERGY, MINIMAL RESTRAINT VIOLATIONS
Conformers calculated total number: 50 / Conformers submitted total number: 32

+
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