Dynarepo 4YEB

Molecular system

Starting structure: 4YEBPDB 4YEB(opens in a new tab)
Force field: CHARMM36mTIP3P
Engine: GROMACS 2024.2
Method: Classical MD
Ensemble: NPT
Temperature: 310 K
Timestep: 2 fs
Composition: Molecules of interest
ProteinProtein · 2 chains9,383 atoms590 residues
Total9,383 atoms590 residues
Box dimensions: Dodecahedron
a11.701nm
b11.701nm
c8.291nm

Sequences

Sequence 1Protein · 269 residues

VFLCPGLLKG VYQSEHLFES DHQSGAWCKD PLQASDKIYY MPWTPYRTDT LTEYSSKDDF IAGRPTTTYK LPHRVDGTGF VVYDGALFFN KERTRNIVKF DLRTRIKSGE AIIANANYHD TSPYRWGGKS DIDLAVDENG LWVIYATEQN NGKIVISQLN PYTLRIEGTW DTAYDKRSAS NAFMICGILY VVKSVYEDDD NEATGNKIDY IYNTDQSKDS LVDVPFPNSY QYIAAVDYNP RDNLLYVWNN YHVVKYSLDF GPLDSRSGP

Sequence 2Protein · 321 residues

SCPSVCRCDA GFIYCNDRSL TSIPVGIPED ATTLYLQNNQ INNVGIPSDL KNLLKVQRIY LYHNSLDEFP TNLPKYVKEL HLQENNIRTI TYDSLSKIPY LEELHLDDNS VSAVSIEEGA FRDSNYLRLL FLSRNHLSTI PGGLPRTIEE LRLDDNRIST ISSPSLHGLT SLKRLVLDGN LLNNHGLGDK VFFNLVNLTE LSLVRNSLTA APVNLPGTSL RKLYLQDNHI NRVPPNAFSY LRQLYRLDMS NNNLSNLPQG IFDDLDNITQ LILRNNPWYC GCKMKWVRDW LQSLPVKVNV RGLMCQAPEK VRGMAIKDLS A

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

Files

67 files

All files

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

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements