MDBind 6gop | MDRepo

Description

10 ns simulation of 6gop pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 6GOPPDB 6GOP(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 · 3 chains10,062 atoms652 residues
OtherOther46 atoms
Total10,111 atoms656 residues
Box dimensions: a7.678nm
b12.782nm
c10.275nm

Sequences

Sequence 1Protein · 226 residues

TTIVGVKFNN GVVIAADTRS TQGPIVADKN CAKLHRISPK IWCAGAGTAA DTEAVTQLIG SNIELHSLYT SREPRVVSAL QMLKQHLFKY QGHIGAYLIV AGVDPTGSHL FSIHAHGSTD VGYYLSLGSG SLAAMAVLES HWKQDLTKEE AIKLASDAIQ AGIWNDLGSG SNVDVCVMEI GKDAEYLRNY LTPNVREEKQ KSYKFPRGTT AVLKESIVNI CDIQEE

Sequence 2Protein · 204 residues

SDPSSINGGI VVAMTGKDCV AIACDLRLGS QSLGVSNKFE KIFHYGHVFL GITGLATDVT TLNEMFRYKT NLYKLKEERA IEPETFTQLV SSSLYERRFG PYFVGPVVAG INSKSGKPFI AGFDLIGCID EAKDFIVSGT ASDQLFGMCE SLYEPNLEPE DLFETISQAL LNAADRDALS GWGAVVYIIK KDEVVKRYLK MRQD

Sequence 3Protein · 222 residues

QFNPYGDNGG TILGIAGEDF AVLAGDTRNI TDYSINSRYE PKVFDCGDNI VMSANGFAAD GDALVKRFKN SVKWYHFDHN DKKLSINSAA RNIQHLLYGK RFFPYYVHTI IAGLDEDGKG AVYSFDPVGS YEREQCRAGG AAASLIMPFL DNQVNFKNQY EPGTNGKVKK PLKYLSVEEV IKLVRDSFTS ATERHIQVGD GLEILIVTKD GVRKEFYELK RD

Experiments

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

Files

32 files · 163 MB

All files163 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