A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 hetero molecules
Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
-
Details
Has ligand of interest
Y
Nonpolymer details
The authors state that the zinc-binding group and hydrophobic core of the inhibitor have weak ...The authors state that the zinc-binding group and hydrophobic core of the inhibitor have weak density in the binding pocket of ENPP1. The piperidinyl linker moiety shows very weak density apparently because of high flexibility of the hydrocarbon and it being exposed to the solvent. In polypeptide chain A the inhibitor was modeled with 0.5 occupancy. Trace of inhibitor in the electron density appears to be present in polypeptide B chain but the density is very weak and the inhibitor wasn't modeled there.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.76 Å3/Da / Density % sol: 55.51 % / Description: Needle
Crystal grow
Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 600, sodium acetate, magnesium acetate, polyvinylpyrrolidone
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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