[English] 日本語
Yorodumi
- PDB-2kp8: Ligand bound to a model peptide that mimics the open fusogenic form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kp8
TitleLigand bound to a model peptide that mimics the open fusogenic form
ComponentsModel peptide
KeywordsUNKNOWN FUNCTION / protein/ligand
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / Chem-XIG
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, Final minimization step
AuthorsOlejniczak, E.T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Non-peptide entry inhibitors of HIV-1 that target the gp41 coiled coil pocket.
Authors: Stewart, K.D. / Huth, J.R. / Ng, T.I. / McDaniel, K. / Hutchinson, R.N. / Stoll, V.S. / Mendoza, R.R. / Matayoshi, E.D. / Carrick, R. / Mo, H. / Severin, J. / Walter, K. / Richardson, P.L. / ...Authors: Stewart, K.D. / Huth, J.R. / Ng, T.I. / McDaniel, K. / Hutchinson, R.N. / Stoll, V.S. / Mendoza, R.R. / Matayoshi, E.D. / Carrick, R. / Mo, H. / Severin, J. / Walter, K. / Richardson, P.L. / Barrett, L.W. / Meadows, R. / Anderson, S. / Kohlbrenner, W. / Maring, C. / Kempf, D.J. / Molla, A. / Olejniczak, E.T.
History
DepositionOct 9, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Model peptide
B: Model peptide
C: Model peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0574
Polymers24,4773
Non-polymers5801
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Model peptide


Mass: 8159.135 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-XIG / 5-{[(4'-methoxybiphenyl-4-yl)methyl][(1S)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}benzene-1,2,4-tricarboxylic acid


Mass: 579.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H29NO8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
NMR detailsText: edited filtered Noesy experiments

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] peptide, 6 mM 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-15N]-vlI methyl13C peptide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMpeptide[U-100% 13C; U-100% 15N]1
6 mM3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE1
1 mMpeptide[U-15N]-vlI methyl13C2
Sample conditionsIonic strength: 25 / pH: 8.0 / Pressure: ambient / Temperature: 318 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameDeveloperClassification
X-PLORBrunger, A.T. et al.geometry optimization
X-PLORBrunger, A.T. et al.refinement
TALOSCornilescu, G. et al.data analysis
SchrodingerSchrodingergeometry optimization
RefinementMethod: simulated annealing, Final minimization step / Software ordinal: 1 / Details: using xplor, using schrodinger
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 5

+
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