Data DOI: 10.15785/SBGRID/190 | ID: 190
Publication DOI: 10.1038/nature09638
3PE4 Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB
Sliz Laboratory, Harvard Medical School
Release Date: 3 Nov 2015
1. If this dataset is locally available, it should be accessable at /programs/datagrid/190
2. To download this dataset, please run the following command from your Terminal on a Linux or OS X workstation:
'rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/190 .' (Harvard Medical School, USA)
Depending on your location, faster access may be available from a Tier 1 site closer to your location
'rsync -av rsync://sbgrid.icm.uu.se/10.15785/SBGRID/190 .' (Uppsala University, Sweden)
'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/190 .' (Institut Pasteur de Montevideo, Uruguay)
'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/190 .' (Shanghai Institutes for Biological Sciences, China)
3. After the transfer is completed, please issue the following command to verify data integrity:
'cd 190 ; shasum -c files.sha'
Storage requirements: 41G
Biological Sample:
human O-GlcNAc transferase
Dataset Type:
Structural Model
Subject Composition:
Protein
Collection Facility:
SBGrid MD Cluster
Data Creation Date:
8 Mar 2010
Related Datasets:
None
Sliz, P. 2015. "human O-GlcNAc transferase. PDB Code 3PE4", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/190.
MD trajectory. The coordinates of the OGT–UDP–peptide complex (PDB 3PE4) were optimized in the Protein Preparation Wizard (Schrodinger 2009) where hydrogens were added; water molecules, UDP and peptide were stripped; and the structure was minimized using the OPLS2001 forcefield. The 1-μm simulation used the CHARM27 forcefield46, and the simple point charge model for water47. The CHARM27 forcefield was applied to the system using the VIPARR utility. The default Desmond relaxation was performed before simulation, and molecular dynamics were run at constant temperature (300 K) and pressure (1 bar). The simulation was performed by using the program Desmond, version 2.2.9.1.030 compiled by SBGrid on an optimized 64-node Linux-based InfiniBand cluster and took 75 days to complete. Molecular dynamics trajectories were processed and animated with VMD48.
| Name | Additional Roles | Affiliation While Working on the Project |
|---|---|---|
| Piotr Sliz | Data Collector, Depositor, PI | Harvard Medical School |
none
License: CC0
Terms: Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation, as generated by the SBGrid Data Bank.
