[English] 日本語
Yorodumi
- PDB-1d0w: SOLUTION STRUCTURE OF LACTAM-BRIDGED C-TERMINAL ANALOGUE-I OF NEU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d0w
TitleSOLUTION STRUCTURE OF LACTAM-BRIDGED C-TERMINAL ANALOGUE-I OF NEUROPEPTIDE Y
ComponentsC-TERMINAL ANALOGUE OF NEUROPEPTIDE Y, A POTENT Y2 RECEPTOR AGONIST
KeywordsNEUROPEPTIDE / LACTAM-BRIDGED / HELIX
MethodSOLUTION NMR / simulated annealing
AuthorsYao, S. / Norton, R.S.
Citation
Journal: J.Med.Chem. / Year: 2002
Title: Stabilization of the helical structure of Y2-selective analogues of neuropeptide Y by lactam bridges.
Authors: Yao, S. / Smith-White, M.A. / Potter, E.K. / Norton, R.S.
#1: Journal: To be Published
Title: Helical structure and self-association in a 13-residue neuropeptide Y Y2 receptor agonist: relationship to biological activity
Authors: Barnham, K.J. / Catalfamo, F. / Pallaghy, P.K. / Howlett, G.J. / Norton, R.S.
#2: Journal: J.Biomol.NMR / Year: 1996
Title: Solution structure of human neuropeptide Y
Authors: Monks, S.A. / Karagianis, G. / Howlett, G.J. / Norton, R.S.
History
DepositionSep 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _struct_conn.details / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-TERMINAL ANALOGUE OF NEUROPEPTIDE Y, A POTENT Y2 RECEPTOR AGONIST


Theoretical massNumber of molelcules
Total (without water)1,7921
Polymers1,7921
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)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide C-TERMINAL ANALOGUE OF NEUROPEPTIDE Y, A POTENT Y2 RECEPTOR AGONIST


Mass: 1792.054 Da / Num. of mol.: 1 / Fragment: C-TERMINAL ANALOGUE
Mutation: L24A, I28K, I31L, T32E, A LACTAM-BRIDGE WAS INTRODUCED BETWEEN POSITIONS (28) AND (32)
Source method: obtained synthetically / Details: Chemically synthesized.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

-
Sample preparation

DetailsContents: 3.5 MG IN 0.6 ML H2O CONTAINING 30% TFE-D3 (BY VOLUME)
Sample conditionspH: 5 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AMXBrukerAMX5002

-
Processing

NMR software
NameVersionDeveloperClassification
XEASY2.1BRUKERcollection
XEASY1.3BARTELSdata analysis
X-PLOR3.85BRUNGERstructure solution
X-PLOR3.85BRUNGERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURE WAS CALCULATED USING A TOTAL OF 124 UPPER BOUND DISTANCE RESTRAINTS AND 8 BACKBONE DIHEDRAL ANGLE CONSTRAINTS
NMR representativeSelection criteria: closest to the average
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