MDBind 6bj3 2 | MDRepo

Description

10 ns simulation of 6bj3 pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 6BJ3PDB 6BJ3(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 · 4 chains12,878 atoms817 residues
OtherOther143 atoms
Total13,021 atoms818 residues
Box dimensions: a11.774nm
b12.032nm
c12.473nm

Sequences

Sequence 1Protein · 275 residues

SHSMRYFYTA MSRPGRGEPR FIAVGYVDDT QFVRFDSDAA SPRTEPRAPW IEQEGPEYWD RNTQIFKTNT QTYRESLRNL RGYYNQSEAG SHIIQRMYGC DLGPDGRLLR GHDQSAYDGK DYIALNEDLS SWTAADTAAQ ITQRKWEAAR VAEQLRAYLE GLCVEWLRRY LENGKETLQR ADPPKTHVTH HPVSDHEATL RCWALGFYPA EITLTWQRDG EDQTQDTELV ETRPAGDRTF QKWAAVVVPS GEEQRYTCHV QHEGLPKPLT LRWEP

Sequence 2Protein · 99 residues

IQRTPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTEF TPTEKDEYAC RVNHVTLSQP KIVKWDRDM

Sequence 3Protein · 202 residues

QKVTQAQSSV SMPVRKAVTL NCLYETSWWS YYIFWYKQLP SKEMIFLIRQ GSDEQNAKSG RYSVNFKKAA KSVALTISAL QLEDSAKYFC ALGEGGAQKL VFGQGTRLTI NPNIQNPDPA VYQLRDSKSS DKSVCLFTDF DSQTNVSQSK DSDVYITDKC VLDMRSMDFK SNSAVAWSNK SDFACANAFN NSIIPEDTFF PS

Sequence 4Protein · 241 residues

GVTQTPKFQV LKTGQSMTLQ CAQDMNHNSM YWYRQDPGMG LRLIYYSASE GTTDKGEVPN GYNVSRLNKR EFSLRLESAA PSQTSVYFCA SRTRGGTLIE QYFGPGTRLT VTEDLKNVFP PEVAVFEPSE AEISHTQKAT LVCLATGFYP DHVELSWWVN GKEVHSGVCT DPQPLKEQPA LNDSRYCLSS RLRVSATFWQ NPRNHFRCQV QFYGLSENDE WTQDRAKPVT QIVSAEAWGR A

Experiments

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

Files

27 files · 187 MB

All files187 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