[English] 日本語
Yorodumi
- PDB-5zvn: Structure of [beta Glc-T9,K7]indolicidin, a glycosylated analogue... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zvn
TitleStructure of [beta Glc-T9,K7]indolicidin, a glycosylated analogue of indolicidin
Componentsglycosylated analogue of Indolicidin
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial Indolicidin derivative
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / defense response to fungus / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / extracellular space
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Cystatin superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / Cathelicidin-4
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / distance geometry
AuthorsDwivedi, R. / Aggarwal, P. / Kaur, K.J. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
DST SR/S1/OC-63/2012 India
CitationJournal: Amino Acids / Year: 2019
Title: Design of therapeutically improved analogue of the antimicrobial peptide, indolicidin, using a glycosylation strategy.
Authors: Dwivedi, R. / Aggarwal, P. / Bhavesh, N.S. / Kaur, K.J.
History
DepositionMay 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: glycosylated analogue of Indolicidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0352
Polymers1,8551
Non-polymers1801
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Mass of peptide is 2014.1858 Daltons
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area300 Å2
ΔGint2 kcal/mol
Surface area2320 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide glycosylated analogue of Indolicidin


Mass: 1855.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P33046*PLUS
#2: Sugar ChemComp-BGC / beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
151isotropic12D 1H-1H NOESY

-
Sample preparation

DetailsType: micelle / Contents: 2 mM Peptide, 90% H2O/10% D2O
Details: 10mM Phosphate Buffer pH 4.7, 400mM DoDecylphosphorylcholine d-38
Label: 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: Peptide / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0.03 mM / Ionic strength err: 0.001 / Label: 1 / pH: 4.7 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 310 K / Temperature err: 0.001

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500.15 MHz / Details: Avance III

-
Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichchemical shift calculation
TopSpinBruker Biospincollection
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichdata analysis
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: distance geometry / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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