[English] 日本語
Yorodumi
- PDB-3ait: RESTRAINED ENERGY REFINEMENT WITH TWO DIFFERENT ALGORITHMS AND FO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ait
TitleRESTRAINED ENERGY REFINEMENT WITH TWO DIFFERENT ALGORITHMS AND FORCE FIELDS OF THE STRUCTURE OF THE ALPHA-AMYLASE INHIBITOR TENDAMISTAT DETERMINED BY NMR IN SOLUTION
ComponentsTENDAMISTAT
KeywordsALPHA-AMYLASE INHIBITOR
Function / homology
Function and homology information


alpha-amylase inhibitor activity
Similarity search - Function
Alpha-amylase inhibitor / Alpha-amylase inhibitor / Alpha-amylase inhibitor superfamily / Alpha amylase inhibitor / Alpha amylase inhibitor / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-amylase inhibitor HOE-467A
Similarity search - Component
Biological speciesStreptomyces tendae (bacteria)
MethodSOLUTION NMR
AuthorsBilleter, M. / Schaumann, T. / Braun, W. / Wuthrich, K.
Citation
Journal: Biopolymers / Year: 1990
Title: Restrained Energy Refinement with Two Different Algorithms and Force Fields of the Structure of the Alpha-Amylase Inhibitor Tendamistat Determined by NMR in Solution
Authors: Billeter, M. / Schaumann, T. / Braun, W. / Wuthrich, K.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Determination of the Complete Three-Dimensional Structure of the Alpha-Amylase Inhibitor Tendamistat in Aqueous Solution by Nuclear Magnetic Resonance and Distance Geometry
Authors: Kline, A.D. / Braun, W. / Wuthrich, K.
#2: Journal: J.Mol.Biol. / Year: 1986
Title: Complete Sequence-Specific 1H Nuclear Magnetic Resonance Assignments for the Alpha-Amylase Polypeptide Inhibitor Tendamistat from Streptomyces Tendae
Authors: Kline, A.D. / Wuthrich, K.
#3: Journal: J.Mol.Biol. / Year: 1986
Title: Studies by 1H Nuclear Magnetic Resonance and Distance Geometry of the Solution Conformation of Tendamistat an Alpha Amylase Inhibitor
Authors: Kline, A.D. / Braun, W. / Wuthrich, K.
#4: Journal: J.Mol.Biol. / Year: 1985
Title: Secondary Structure of the Alpha-Amylase Polypeptide Inhibitor Tendamistat from Streptomyces Tendae Determined in Solution by 1H Nuclear Magnetic Resonance
Authors: Kline, A.D. / Wuthrich, K.
History
DepositionMay 14, 1990Processing site: BNL
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TENDAMISTAT


Theoretical massNumber of molelcules
Total (without water)7,9681
Polymers7,9681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein TENDAMISTAT


Mass: 7967.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tendae (bacteria) / References: UniProt: P01092
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

SoftwareName: AMBER / Classification: refinement
NMR ensembleConformers submitted total number: 1

+
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