MDBind 5d7e 2

Open

Pierre-yves Libouban;Pascal Bonnet;Samia Aci-Sèche;

MD-A007E9

Created: 17 Feb 2026
License: This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License (opens in a new tab)

Description

10 ns simulation of 5d7e pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 5D7EPDB 5D7E(opens in a new tab)
Force field: Amber ff14SB, GAFFTIP3P
Engine: Amber 20
Method: Classical MD
Timestep: 2 fs
Frames: 500
Composition: Molecules of interest
ProteinProtein · 1 chain2,275 atoms140 residues
OtherOther123 atoms
Total2,398 atoms141 residues
Box dimensions: a5.558nm
b7.766nm
c5.428nm

Sequences

Sequence 1Protein · 140 residues

LGSMVATVKR TIRIKTQQHI LPEVPPVENF PVRQWSIEIV LLDDEGKEIP ATIFDKVIYH LHPTFANPNR TFTDPPFRIE EQGWGGFPLD ISVFLLEKAG ERKIPHDLNF LQESYEVEHV IQIPLNKPLL TEELAKSGST

Run	Outputs
replica 1	Trajectory Analyses
replica 2	Trajectory Analyses
replica 3	Trajectory Analyses
replica 4	Trajectory Analyses
replica 5	Trajectory Analyses
replica 6	Trajectory Analyses
replica 7	Trajectory Analyses
replica 8	Trajectory Analyses
replica 9	Trajectory Analyses
replica 10	Trajectory Analyses

Files

17 files · 31.9 MB

All files31.9 MB

trajectory.binBIN
pca_trajectory_01.binBIN
pca_trajectory_02.binBIN
pca_trajectory_03.binBIN
pca_trajectory_04.binBIN
pca_trajectory_05.binBIN
pca_trajectory_06.binBIN
pca_trajectory_07.binBIN
pca_trajectory_08.binBIN
structure.pdbPDB

Contributors

Research groups: Institute of Organic and Analytical chemistry, Orleans, FranceJanssen/Johnson & Johnson
Contact: For any questions please send a mail to plibouba@its.jnj.com