[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleMolecular insights of acarbose metabolization catalyzed by acarbose-preferred glucosidase.
Journal, issue, pagesNat Commun, Vol. 16, Page 7839-7839, Year 2025
Publish dateJul 24, 2024 (structure data deposition date)
AuthorsHuang, J. / Shen, Z. / Xiao, X. / Wang, L. / Zhang, J. / Zhou, J. / Gu, Y.
External linksNat Commun / PubMed:40846838
MethodsX-ray diffraction
Resolution1.87 - 2.67 Å
Structure data

PDB-9ivz:
Apg mutant enzyme D448A of acarbose hydrolase from human gut flora K. grimontii TD1, complex with acarbose
Method: X-RAY DIFFRACTION / Resolution: 2.29 Å

PDB-9ixh:
Apg mutant enzyme D448A of the human gut flora K. grimontii TD1 acarbose hydrolase
Method: X-RAY DIFFRACTION / Resolution: 2.43 Å

PDB-9ixw:
Apg, crystal structure of acarbose hydrolase from the human gut flora K. grimontii TD1
Method: X-RAY DIFFRACTION / Resolution: 2.32 Å

PDB-9ize:
Acarbose hydrolase from human gut microbiota K. grimontii TD1, Apg mutant enzyme D336A, complexed with acarviosine-glucose
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

PDB-9izo:
Apg mutant enzyme D336A of acarbose hydrolase from human gut flora K. grimontii TD1, complex with acarviosine
Method: X-RAY DIFFRACTION / Resolution: 2.13 Å

PDB-9uns:
Apg mutant enzyme D448N of acarbose hydrolase from human gut flora K. grimontii TD1,complex with acarbose
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-9v0i:
Apg mutant enzyme D448N of the human gut flora K. grimontii TD1 acarbose hydrolase
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-9vd8:
Structure of a truncated loopA mutant from the human gut flora K. grimontii Apg in complex with glucose
Method: X-RAY DIFFRACTION / Resolution: 2.39 Å

PDB-9vdg:
Structure of a truncated loopB mutant from the human gut flora K. grimontii Apg
Method: X-RAY DIFFRACTION / Resolution: 2.67 Å

PDB-9vdw:
Structure of truncated loopA and loopB mutants from the human gut flora K. grimontii Apg
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

Chemicals

ChemComp-HOH:
WATER

PDB-1eax:
Crystal structure of MTSP1 (matriptase)

ChemComp-GLC:
alpha-D-glucopyranose

Source
  • klebsiella grimontii (bacteria)
  • synthetic construct (others)
KeywordsHYDROLASE / complex. / Hydolase / Complex

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more