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Published May 2025 | Version v1
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Human dopamine transporter embedded in a membrane, bound to MDMA 250ns

Creators

  • 1. University of Roehampton

Description

A trio of trajectories are supplied whose data was published in Sahai, M.A. et. al. 2017. They include the human dopamine transporter (hDAT), imbedded in a membrane, bound to amphetamine, MDMA and the new psychoactive substance (NPS) 5-MAPB. In VMD the segid for these compounds are AMP, MDMA and MAPB, respectively, If you align all three trajectories on the protein backbone they can be compared with respect to destabilisation of the second sodium NA2 in the binding site. Residues of importance can be found in Fig 5 and 6 of the attached paper. Any questions please direct them to Michelle Sahai: michelle.sahai@roehampton.ac.uk.

Monovalent neutralising ionic environment.

Trajectory originally donated to SlimMD

Files

snapshot.png

Files (72.3 MB)

Name Size Download all
md5:ca131996940df0dea6e278b4df7f5721
59.8 MB Download
md5:0e1b1a94a64463d1745aae1ec5461025
10.9 MB Download
md5:b6e1e7f59d5b72643e2ffcd844373cdd
634 Bytes Download
md5:382067ea5c816b5c672983513cb96559
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Additional details

Identifiers

DOI
10.1016/j.pnpbp.2016.11.004

Domain Specific Metadata

 
Property Value
Software ACEMD
Molecular Model atomistic
Simulation Method classical
Timestep 4 femtoseconds
Framestep 2.5 nanoseconds
Length 0.25 microseconds
Temperature 310 K
Ensemble NVT
Box Type cubic
Trajectories Cartesian coordinates
Force Fields CHARMM27 (protein), CHARMM36 (lipids), TIP3P (water)
Experimental Structures https://www.rcsb.org/structure/4M48
Membrane Yes
Ligands https://pubchem.ncbi.nlm.nih.gov/compound/MDMA
Sequences MSKSKCSVGLMSSVVAPAKEPNAVGPKEVELILVKEQNGVQLTSSTLTNPRQSPVEAQDRETWGKKIDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYLLFMVIAGMPLFYMELALGQFNREGAAGVWKICPILKGVGFTVILISLYVGFFYNVIIAWALHYLFSSFTTELPWIHCNNSWNSPNCSDAHPGDSSGDSSGLNDTFGTTPAAEYFERGVLHLHQSHGIDDLGPPRWQLTACLVLVIVLLYFSLWKGVKTSGKVVWITATMPYVVLTALLLRGVTLPGAIDGIRAYLSVDFYRLCEASVWIDAATQVCFSLGVGFGVLIAFSSYNKFTNNCYRDAIVTTSINSLTSFSSGFVVFSFLGYMAQKHSVPIGDVAKDGPGLIFIIYPEAIATLPLSSAWAVVFFIMLLTLGIDSAMGGMESVITGLIDEFQLLHRHRELFTLFIVLATFLLSLFCVTNGGIYVFTLLDHFAAGTSILFGVLIEAIGVAWFYGVGQFSDDIQQMTGQRPSLYWRLCWKLVSPCFLLFVVVVSIVTFRPPHYGAYIFPDWANALGWVIATSSMAMVPIYAAYKFCSLPGSFREKLAYAIAPEKDRELVDRGEVRQFTLRHWLKV
Box Dimensions 97.0 x 99.2 x 155.1 Angstrom, alpha: 90.0, beta: 90.0, gamma: 90.0 degrees
Long Range Cutoff 12 Angstrom
Thermostat Langevin
Barostat N/A
Atom Count 46981