MDBind 4qlu | MDRepo

Description

10 ns simulation of 4qlu pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 4QLUPDB 4QLU(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 · 5 chains19,780 atoms1,261 residues
LipidsLipid94 atoms1 residues
Total19,875 atoms1,263 residues
Box dimensions: a10.922nm
b11.954nm
c12.104nm

Sequences

Sequence 1Protein · 195 residues

MDIILGIRVQ DSVILASSKA VTRGISVLKD SDDKTRQLSP HTLMSFAGEA GDTVQFAEYI QANIQLYSIR EDYELSPQAV SSFVRQELAK SIRSRRPYQV NVLIGGYDKK KNKPELYQID YLGTKVELPY GAHGYSGFYT FSLLDHHYRP DMTTEEGLDL LKLCVQELEK RMPMDFKGVI VKIVDKDGIR QVDDF

Sequence 2Protein · 212 residues

TTTLAFRFQG GIIVAVDSRA TAGNWVASQT VKKVIEINPF LLGTMAGGAA DCQFWETWLG SQCRLHELRE KERISVAAAS KILSNLVYQY KGAGLSMGTM ICGYTRKEGP TIYYVDSDGT RLKGDIFCVG SGQTFAYGVL DSNYKWDLSV EDALYLGKRS ILAAAHRDAY SGGSVNLYHV TEDGWIYHGN HDVGELFWKV KEEEGSFNNV IG

Sequence 3Protein · 222 residues

QFNPYGDNGG TILGIAGEDF AVLAGDTRNI TDYSINSRYE PKVFDCGDNI VMSANGFAAD GDALVKRFKN SVKWYHFDHN DKKLSINSAA RNIQHLLYGK RFFPYYVHTI IAGLDEDGKG AVYSFDPVGS YEREQCRAGG AAASLIMPFL DNQVNFKNQY EPGTNGKVKK PLKYLSVEEV IKLVRDSFTS ATERHIQVGD GLEILIVTKD GVRKEFYELK RD

Sequence 4Protein · 233 residues

TQQPIVTGTS VISMKYDNGV IIAADNLGSY GSLLRFNGVE RLIPVGDNTV VGISGDISDM QHIERLLKDL VTENAYDNPL ADAEEALEPS YIFEYLATVM YQRRSKMNPL WNAIIVAGVQ SNGDQFLRYV NLLGVTYSSP TLATGFGAHM ANPLLRKVVD RESDIPKTTV QVAEEAIVNA MRVLYYRDAR SSRNFSLAII DKNTGLTFKK NLQVENMKWD FAKDIKGYGT QKI

Sequence 5Protein · 204 residues

SDPSSINGGI VVAMTGKDCV AIACDLRLGS QSLGVSNKFE KIFHYGHVFL GITGLATDVT TLNEMFRYKT NLYKLKEERA IEPETFTQLV SSSLYERRFG PYFVGPVVAG INSKSGKPFI AGFDLIGCID EAKDFIVSGT ASDQLFGMCE SLYEPNLEPE DLFETISQAL LNAADRDALS GWGAVVYIIK KDEVVKRYLK MRQD

Experiments

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

Files

26 files · 302 MB

All files302 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