2021 Jun 16 Maintance Complete

human O-GlcNAc transferase

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: Nov. 3, 2015

Data Access Instructions

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:

March 8, 2010

Related Datasets:

None


Cite this Dataset

Sliz, P. 2015. "human O-GlcNAc transferase. PDB Code 3PE4", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/190.

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Dataset Description

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.

Project Members

Name Additional Roles Affiliation While Working on the Project
Piotr SlizData Collector, Depositor, PIHarvard Medical School

Reprocessing Instructions

none


License and Terms of use

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.