MDBind 4qwr | MDRepo

Description

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

Molecular system

Starting structure: 4QWRPDB 4QWR(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 chains9,996 atoms648 residues
OtherOther114 atoms
Total10,114 atoms653 residues
Box dimensions: a7.923nm
b11.706nm
c10.018nm

Sequences

Sequence 1Protein · 222 residues

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

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

30 files · 168 MB

All files168 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