MDBind 3p4r | MDRepo

Description

10 ns simulation of 3p4r pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 3P4RPDB 3P4R(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 chains16,583 atoms1,069 residues
OtherOther15 atoms
Total16,598 atoms1,070 residues
Box dimensions: a10.21nm
b9.204nm
c13.189nm

Sequences

Sequence 1Protein · 577 residues

MQTFQADLAI VGAGGAGLRA AIAAAQANPN AKIALISKVY PMRSHTVAAE GGSAAVAQDH DSFEYHFHDT VAGGDWLCEQ DVVDYFVHHC PTEMTQLELW GCPWSRRPDG SVNVRRFGGM KIERTWFAAD KTGFHMLHTL FQTSLQFPQI QRFDEHFVLD ILVDDGHVRG LVAMNMMEGT LVQIRANAVV MATGGAGRVY RYNTNGGIVT GDGMGMALSH GVPLRDMEFV QYHPTGLPGS GILMTEGCRG EGGILVNKNG YRYLQDYGMG PETPLGEPKN KYMELGPRDK VSQAFWHEWR KGNTISTPRG DVVYLDLRHL GEKKLHERLP FICELAKAYV GVDPVKEPIP VRPTAHYTMG GIETDQNCET RIKGLFAVGE CSSVGLHGAN RLGSNSLAEL VVFGRLAGEQ ATERAATAGN GNEAAIEAQA AGVEQRLKDL VNQDGGENWA KIRDEMGLAM EEGCGIYRTP ELMQKTIDKL AELQERFKRV RITDTSSVFN TDLLYTIELG HGLNVAECMA HSAMARKESR GAHQRLDEGC TERDDVNFLK HTLAFRDADG TTRLEYSDVK ITTLPPA

Sequence 2Protein · 243 residues

AEMKNLKIEV VRYNPEVDTA PHSAFYEVPY DATTSLLDAL GYIKDNLAPD LSYRWSCRMA ICGSCGMMVN NVPKLACKTF LRDYTDGMKV EALANFPIER DLVVDMTHFI ESLEAIKPYI IGNSRTADQG TNIQTPAQMA KYHQFSGCIN CGLCYAACPQ FGLNPEFIGP AAITLAHRYN EDSRDHGKKE RMAQLNSQNG VWSCTFVGYC SEVCPKHVDP AAAIQQGKVE SSKDFLIATL KPR

Sequence 3Protein · 130 residues

TTKRKPYVRP MTSTWWKKLP FYRFYMLREG TAVPAVWFSI ELIFGLFALK NGPEAWAGFV DFLQNPVIVI INLITLAAAL LHTKTWFELA PKAANIIVKD EKMGPEPIIK SLWAVTVVAT IVILFVALYW

Sequence 4Protein · 119 residues

MINPNPKRSD EPVFWGLFGA GGMWSAIIAP VMILLVGILL PLGLFPGDAL SYERVLAFAQ SFIGRVFLFL MIVLPLWCGL HRMHHAMHDL KIHVPAGKWV FYGLAAILTV VTLIGVVTI

Experiments

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

Files

34 files · 284 MB

All files284 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