MDBind 5umz

10 ns simulation of 5umz pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 5UMZPDB 5UMZ(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 chain6,568 atoms426 residues
OtherOther159 atoms
Total6,727 atoms427 residues
Box dimensions: a6.751nm
b10.289nm
c10.253nm

Sequences

Sequence 1Protein · 426 residues

GTVNWSVEDI VKGINSNNLE SQLQATQAAR KLLSREKQPP IDNIIRAGLI PKFVSFLGKT DCSPIQFESA WALTNIASGT SEQTKAVVDG GAIPAFISLL ASPHAHISEQ AVWALGNIAG DGSAFRDLVI KHGAIDPLLA LLAVPDLSTL ACGYLRNLTW TLSNLCRNKN PAPPLDAVEQ ILPTLVRLLH HNDPEVLADS CWAISYLTDG PNERIEMVVK KGVVPQLVKL LGATELPIVT PALRAIGNIV TGTDEQTQKV IDAGALAVFP SLLTNPKTNI QKEATWTMSN ITAGRQDQIQ QVVNHGLVPF LVGVLSKADF KTQKEAAWAI TNYTSGGTVE QIVYLVHCGI IEPLMNLLSA KDTKIIQVIL DAISNIFQAA EKLGETEKLS IMIEECGGLD KIEALQRHEN ESVYKASLNL IEKYFS

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

29 files · 100 MB

All files100 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