MDBind 3d9n

Open

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

MD-A0064Y

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 3d9n pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 3D9NPDB 3D9N(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 chain2,289 atoms138 residues
OtherOther91 atoms
Total2,380 atoms139 residues
Box dimensions: a5.729nm
b6.075nm
c6.916nm

Sequences

Sequence 1Protein · 138 residues

EAVKTFNSEL YSLNDYKPPI SKAKMTQITK AAIKAIKFYK HVVQSVEKFI QKCKPEYKVP GLYVIDSIVR QSRHQFGQEK DVFAPRFSNN IISTFQNLYR CPGDDKSKIV RVLNLWQKNN VFKSEIIQPL LDMAAALE

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

37 files · 43 MB

All files43 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
pca_trajectory_09.binBIN

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