MDBind 1sqq

Pierre-yves Libouban,Pascal Bonnet,Samia Aci-Sèche

Created 17 Feb 2026Updated 29 Jun 2026This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License

MD-A00653

Description

10 ns simulation of 1sqq pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 1SQQPDB 1SQQ(opens in a new tab)
Program: Amber 20
Force field: Amber ff14SB, GAFF
Water model: TIP3P
Method: Classical MD
Timestep: 2 fs
Frames: 500
Size: 65,976 atoms

Sequences

Sequence 1Protein · 446 residues

TATYAQALQS VPETQVSQLD NGLRVASEQS SQPTCTVGVW IDAGSRYESE KNNGAGYFVE HLAFKGTKNR PGNALEKEVE SMGAHLNAYS TREHTAYYIK ALSKDLPKAV ELLADIVQNC SLEDSQIEKE RDVILQELQE NDTSMRDVVF NYLHATAFQG TPLAQSVEGP SENVRKLSRA DLTEYLSRHY KAPRMVLAAA GGLEHRQLLD LAQKHFSGLS GTYDEDAVPT LSPCRFTGSQ ICHREDGLPL AHVAIAVEGP GWAHPDNVAL QVANAIIGHY DCTYGGGAHL SSPLASIAAT NKLCQSFQTF NICYADTGLL GAHFVCDHMS IDDMMFVLQG QWMRLCTSAT ESEVLRGKNL LRNALVSHLD GTTPVCEDIG RSLLTYGRRI PLAEWESRIA EVDARVVREV CSKYFYDQCP AVAGFGPIEQ LPDYNRIRSG MFWLRF

Sequence 2Protein · 423 residues

VPPHPQDLEF TRLPNGLVIA SLENYAPASR IGLFIKAGSR YENSNNLGTS HLLRLASSLT TKGASSFKIT RGIEAVGGKL SVTSTRENMA YTVECLRDDV DILMEFLLNV TTAPEFRRWE VAALQPQLRI DKAVALQNPQ AHVIENLHAA AYRNALANSL YCPDYRIGKV TPVELHDYVQ NHFTSARMAL IGLGVSHPVL KQVAEQFLNI RGGLGLSGAK AKYHGGEIRE QNGDSLVHAA LVAESAAIGS AEANAFSVLQ HVLGAGPHVK RGSNATSSLY QAVAKGVHQP FDVSAFNASY SDSGLFGFYT ISQAASAGDV IKAAYNQVKT IAQGNLSNPD VQAAKNKLKA GYLMSVESSE GFLDEVGSQA LAAGSYTPPS TVLQQIDAVA DADVINAAKK FVSGRKSMAA SGNLGHTPFI DEL

Sequence 3Protein · 378 residues

TNIRKSHPLM KIVNNAFIDL PAPSNISSWW NFGSLLGICL ILQILTGLFL AMHYTSDTTT AFSSVTHICR DVNYGWIIRY MHANGASMFF ICLYMHVGRG LYYGSYTFLE TWNIGVILLL TVMATAFMGY VLPWGQMSFW GATVITNLLS AIPYIGTNLV EWIWGGFSVD KATLTRFFAF HFILPFIIMA IAMVHLLFLH ETGSNNPTGI SSDVDKIPFH PYYTIKDILG ALLLILALML LVLFAPDLLG DPDNYTPANP LNTPPHIKPE WYFLFAYAIL RSIPNKLGGV LALAFSILIL ALIPLLHTSK QRSMMFRPLS QCLFWALVAD LLTLTWIGGQ PVEHPYITIG QLASVLYFLL ILVLMPTAGT IENKLLKW

Sequence 4Protein · 241 residues

SDLELHPPSY PWSHRGLLSS LDHTSIRRGF QVYKQVCSSC HSMDYVAYRH LVGVCYTEDE AKALAEEVEV QDGPNEDGEM FMRPGKLSDY FPKPYPNPEA ARAANNGALP PDLSYIVRAR HGGEDYVFSL LTGYCEPPTG VSLREGLYFN PYFPGQAIGM APPIYNEVLE FDDGTPATMS QVAKDVCTFL RWAAEPEHDH RKRMGLKMLL MMGLLLPLVY AMKRHKWSVL KSRKLAYRPP K

Sequence 5Protein · 196 residues

SHTDIKVPDF SDYRRPEVLD STKSSKESSE ARKGFSYLVT ATTTVGVAYA AKNVVSQFVS SMSASADVLA MSKIEIKLSD IPEGKNMAFK WRGKPLFVRH RTKKEIDQEA AVEVSQLRDP QHDLERVKKP EWVILIGVCT HLGCVPIANA GDFGGYYCPC HGSHYDASGR IRKGPAPLNL EVPSYEFTSD DMVIVG

Sequence 6Protein · 105 residues

VSASSRWLEG IRKWYYNAAG FNKLGLMRDD TIHENDDVKE AIRRLPENLY DDRVFRIKRA LDLSMRQQIL PKEQWTKYEE DKSYLEPYLK EVIRERKERE EWAKK

Sequence 7Protein · 75 residues

GRQFGHLTRV RHVITYSLSP FEQRAFPHYF SKGIPNVLRR TRACILRVAP PFVAFYLVYT WGTQEFEKSK RKNPA

Sequence 8Protein · 70 residues

EEEELVDPLT TVREQCEQLE KCVKARERLE LCDERVSSRS QTEEDCTEEL LDFLHARDHC VAHKLFNSLK

Sequence 9Protein · 57 residues

MLSVAARSGP FAPVLSATSR GVAGALRPLV QAAVPATSES PVLDLKRSVL CRESLRG

Sequence 10Protein · 59 residues

PTLTARLYSL LFRRTSTFAL TIVVGALFFE RAFDQGADAI YEHINEGKLW KHIKHKYEN

Sequence 11Protein · 54 residues

MLTRFLGPRY RQLARNWVPT ASLWGAVGAV GLVWATDWRL ILDWVPYING KFKK

Experiments

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

Files

37 files · 1.2 GB

All files1.2 GB

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