MDBind 4pgb 1 | MDRepo

Description

10 ns simulation of 4pgb pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 4PGBPDB 4PGB(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 · 2 chains6,029 atoms377 residues
OtherOther135 atoms
Total6,164 atoms378 residues
Box dimensions: a9.14nm
b7.419nm
c8.423nm

Sequences

Sequence 1Protein · 278 residues

GPHSLRYFVT AVSRPGLGEP RYMEVGYVDD TEFVRFDSDA ENPRYEPRAR WMEQEGPEYW ERETQKAKGN EQSFRVDLRT LLGYYNQSKG GSHTIQVISG CEVGSDGRLL RGYQQYAYDG CDYIALNEDL KTWTAADMAA LITKHKWEQA GEAERLRAYL EGTCVEWLRR YLKNGNATLL RTDSPKAHVT HHSRPEDKVT LRCWALGFYP ADITLTWQLN GEELIQDMEL VETRPAGDGT FQKWASVVVP LGKEQYYTCH VYHQGLPEPL TLRWEPPP

Sequence 2Protein · 99 residues

IQKTPQIQVY SRHPPENGKP NILNCYVTQF HPPHIEIQML KNGKKIPKVE MSDMSFSKDW SFYILAHTEF TPTETDTYAC RVKHDSMAEP KTVYWDRDM

Experiments

Run	Outputs
replica 1	Trajectory Analyses
replica 2	Trajectory Analyses
replica 3

Files

31 files · 91.6 MB

All files91.6 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