MDBind 3o4l | MDRepo

Description

10 ns simulation of 3o4l pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 3O4LPDB 3O4L(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 chains12,764 atoms816 residues
OtherOther135 atoms
Total12,899 atoms817 residues
Box dimensions: a9.505nm
b15.05nm
c7.874nm

Sequences

Sequence 1Protein · 276 residues

GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQRMEPRAP WIEQEGPEYW DGETRKVKAH SQTHRVDLGT LRGYYNQSEA GSHTVQRMYG CDVGSDWRFL RGYHQYAYDG KDYIALKEDL RSWTAADMAA QTTKHKWEAA HVAEQLRAYL EGTCVEWLRR YLENGKETLQ RTDAPKTHMT HHAVSDHEAT LRCWALSFYP AEITLTWQRD GEDQTQDTEL VETRPAGDGT FQKWAAVVVP SGQEQRYTCH VQHEGLPKPL TLRWEP

Sequence 2Protein · 100 residues

MIQRTPKIQV YSRHPAENGK SNFLNCYVSG FHPSDIEVDL LKNGERIEKV EHSDLSFSKD WSFYLLYYTE FTPTEKDEYA CRVNHVTLSQ PCIVKWDRDM

Sequence 3Protein · 195 residues

QSLFLSVREG DSSVINCTYT DSSSTYLYWY KQEPGAGLQL LTYIFSNMDM KQDQRKTVLL NKKDKHLSLR IADTQTGDSA IYFCAEDNNA RLMFGDGTQL VVKPNIQNPD PAVYQLRDSK SSDKSVCLFT DFDSQTNVSQ SKDSDVYITD KCVLDMRSMD FKSNSAVAWS NKSDFACANA FNNSIIPEDT FFPSP

Sequence 4Protein · 245 residues

GAVVSQHPSW VICKSGTSVK IECRSLDFQA TTMFWYRQFP KQSLMLMATS NEGSKATYEQ GVEKDKFLIN HASLTLSTLT VTSAHPEDSS FYICSARDGT GNGYTFGSGT RLTVVEDLNK VFPPEVAVFE PSEAEISHTQ KATLVCLATG FYPDHVELSW WVNGKEVHSG VCTDPQPLKE QPALNDSRYA LSSRLRVSAT FWQDPRNHFR CQVQFYGLSE NDEWTQDRAK PVTQIVSAEA WGRAD

Experiments

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

Files

28 files · 191 MB

All files191 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