MDBind 3q5u

10 ns simulation of 3q5u pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 3Q5UPDB 3Q5U(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 · 1 chain6,531 atoms423 residues
OtherOther143 atoms
Total6,674 atoms424 residues
Box dimensions: a6.672nm
b10.29nm
c10.031nm

Sequences

Sequence 1Protein · 423 residues

NWSVEDIVKG INSNNLESQL QATQAARKLL SREKQPPIDN IIRAGLIPKF VSFLGKTDCS PIQFESAWAL TNIASGTSEQ TKAVVDGGAI PAFISLLASP HAHISEQAVW ALGNIAGDGS AFRDLVIKHG AIDPLLALLA VPDLSTLACG YLRNLTWTLS NLCRNKNPAP PLDAVEQILP TLVRLLHHND PEVLADSCWA ISYLTDGPNE RIEMVVKKGV VPQLVKLLGA TELPIVTPAL RAIGNIVTGT DEQTQKVIDA GALAVFPSLL TNPKTNIQKE ATWTMSNITA GRQDQIQQVV NHGLVPFLVG VLSKADFKTQ KEAAWAITNY TSGGTVEQIV YLVHCGIIEP LMNLLSAKDT KIIQVILDAI SNIFQAAEKL GETEKLSIMI EECGGLDKIE ALQRHENESV YKASLNLIEK YFS

Run	Outputs
replica 1	Trajectory Analyses
replica 2	Trajectory Analyses
replica 3	Trajectory Analyses
replica 4	Trajectory Analyses
replica 5	Trajectory Analyses
replica 6	Trajectory Analyses
replica 7	Trajectory Analyses
replica 8	Trajectory Analyses
replica 9	Trajectory Analyses
replica 10	Trajectory Analyses

Files

30 files · 99 MB

All files99 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

Description

Molecular system

Sequences

Experiments

Files

Contributors