MDBind 6b5m | MDRepo

Description

10 ns simulation of 6b5m pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 6B5MPDB 6B5M(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 chains6,590 atoms437 residues
OtherOther179 atoms
Total6,769 atoms438 residues
Box dimensions: a7.878nm
b7.382nm
c10.241nm

Sequences

Sequence 1Protein · 220 residues

VQLVQSGAEV KKPGASVKVS CKASGYTFTS YAIHWVRQAP GQRLEWMGWI KAGNGNTRYS QKFQDRVTIT RDTSTTTAYM ELSSLRSEDT AVYYCALLTV LTPDDAFDIW GQGTMVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP

Sequence 2Protein · 217 residues

DIVMTQSPDS LAVSLGERAT INCKSSQSVL YSSNNKNYLA WYQQKPGQPP NLLIYWASTR QSGVPDRFSG SGSGTDFTLT ISSLQAEDVA VYYCHQYYSS PLTFGGGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNR

Experiments

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

Files

30 files · 110 MB

All files110 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