[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 mechanism of activation of the immunoregulatory amidase NAAA.
Journal, issue, pagesProc. Natl. Acad. Sci. U.S.A., Vol. 115, Page E10032-E10040, Year 2018
Publish dateJul 1, 2018 (structure data deposition date)
AuthorsGorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B.
External linksProc. Natl. Acad. Sci. U.S.A. / PubMed:30301806
MethodsX-ray diffraction
Resolution1.851 - 3.014 Å
Structure data

PDB-6dxw:
Human N-acylethanolamine-hydrolyzing acid amidase (NAAA) precursor (C126A)
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-6dxx:
Human N-acylethanolamine-hydrolyzing acid amidase (NAAA) in complex with non-covalent benzothiazole-piperazine inhibitor ARN19702, in presence of Triton X-100
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-6dxy:
Murine N-acylethanolamine-hydrolyzing acid amidase (NAAA)
Method: X-RAY DIFFRACTION / Resolution: 1.851 Å

PDB-6dxz:
Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) in complex with non-covalent benzothiazole-piperazine inhibitor ARN19702, in presence of Triton X-100
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-6dy0:
Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) covalently bound to beta-lactam inhibitor ARN726, in presence of Triton X-100
Method: X-RAY DIFFRACTION / Resolution: 3.014 Å

PDB-6dy1:
Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) with fatty acid (myristate), in presence of Triton X-100
Method: X-RAY DIFFRACTION / Resolution: 2.998 Å

PDB-6dy2:
Guinea pig N-acylethanolamine-hydrolyzing acid amidase (NAAA) covalently bound to beta-lactam inhibitor ARN726
Method: X-RAY DIFFRACTION / Resolution: 2.706 Å

PDB-6dy3:
Caenorhabditis elegans N-acylethanolamine-hydrolyzing acid amidase (NAAA) ortholog
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-CL:
Unknown entry / Chloride

ChemComp-HOH:
WATER / Water

ChemComp-TON:
2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL

ChemComp-WTF:
[2-(ethylsulfonyl)phenyl][(2S)-4-(6-fluoro-1,3-benzothiazol-2-yl)-2-methylpiperazin-1-yl]methanone

ChemComp-SCN:
THIOCYANATE ION / Thiocyanate

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-P33:
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / precipitant*YM / Polyethylene glycol

ChemComp-K:
Unknown entry

ChemComp-TRT:
FRAGMENT OF TRITON X-100 / detergent*YM / Triton X-100

ChemComp-27L:
4-(2,4,4-trimethylpentan-2-yl)phenol

ChemComp-HJA:
(2S)-3-amino-2-{[(4-cyclohexylbutoxy)carbonyl]amino}propanethioic S-acid

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-MYR:
MYRISTIC ACID / Myristic acid

ChemComp-PO4:
PHOSPHATE ION / Phosphate

Source
  • homo sapiens (human)
  • mus musculus (house mouse)
  • oryctolagus cuniculus (rabbit)
  • cavia porcellus (domestic guinea pig)
  • caenorhabditis elegans (invertebrata)
KeywordsHYDROLASE / endocannabinoid / lipase

+
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