MDBind 4j8r 2 | MDRepo

Description

10 ns simulation of 4j8r pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 4J8RPDB 4J8R(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 chains6,402 atoms429 residues
OtherOther121 atoms
Total6,523 atoms430 residues
Box dimensions: a8.89nm
b7.345nm
c8.735nm

Sequences

Sequence 1Protein · 209 residues

DIVMTQSHKF MSTSVGDRVS ITCKASQVGT ALAWYQQKPG QSPKLLIYWA STRHTGVPDR FTGSGSGTDF TLTISNVQSE DLSDYFCQQY SSYPTFGGGT KLEIKRADAA PTVSIFPPSS EQLTSGGASV VCFLNNFYPK DINVKWKIDG SERQNGVLNS ETDQDSKDST YSMSSTLTLT KDEYERHNSY TCEATHKTST SPIVKSFNR

Sequence 2Protein · 220 residues

VKLQESGGEV VRPGTSVKVS CKASGYAFTN YLIEWVKQRP GQGLEWIGVI NPGSGDTNYN EKFKGKATLT ADKSSSTAYM QLNSLTSDDS AVYFCARSGA AAPTYYAMDY WGQGVSVTVS SAKTTPPSVY PLAPAAAAAN SMVTLGCLVK GYFPEPVTVT WNSGSLSGGV HTFPAVLQSD LYTLSSSVTV PSSTWPSETV TCNVAHPASS TKVDKKIVPR

Experiments

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

Files

28 files · 96.6 MB

All files96.6 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