MDBind 5u98 | MDRepo

Description

10 ns simulation of 5u98 pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 5U98PDB 5U98(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 chains5,931 atoms372 residues
OtherOther149 atoms
Total6,080 atoms373 residues
Box dimensions: a7.3nm
b8.941nm
c9.238nm

Sequences

Sequence 1Protein · 273 residues

SHSMRYFYTA MSRPGRGEPR FIAVGYVDDT QFVRFDSDAA SPRMAPRAPW IEQEGPEYWD GETRNMKASA QTYRENLRIA LRYYNQSEAG SHIIQVMYGC DVGPDGRLLR GHDQSAYDGK DYIALNEDLS SWTAADTAAQ ITQRKWEAAR VAEQLRAYLE GLCVEWLRRY LENGKETLQR ADPPKTHVTH HPISDHEATL RCWALGFYPA EITLTWQRDG EDQTQDTELV ETRPAGDRTF QKWAAVVVPS GEEQRYTCHV QHEGLPKPLT LRW

Sequence 2Protein · 99 residues

IQRTPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTEF TPTEKDEYAC RVNHVTLSQP KIVKWDRDM

Experiments

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

Files

33 files · 101 MB

All files101 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