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- PDB-2lps: Molecular dynamics re-refinement of domain 5 of the yeast ai5(gam... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2lps | ||||||
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Title | Molecular dynamics re-refinement of domain 5 of the yeast ai5(gamma) group II intron | ||||||
![]() | RNA (34-MER) | ||||||
![]() | RNA / Tetraloop / Bulge | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | closest to the average, model 1 | ||||||
![]() | Henriksen, N.M. / Davis, D.R. / Cheatham III, T.E. | ||||||
![]() | ![]() Title: Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Authors: Sigel, R.K. / Sashital, D.G. / Abramovitz, D.L. / Palmer, A.G. / Butcher, S.E. / Pyle, A.M. | ||||||
History |
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Remark 0 | THIS ENTRY 2LPS REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (1R2P.MR) ... THIS ENTRY 2LPS REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (1R2P.MR) DETERMINED BY AUTHORS OF THE PDB ENTRY 1R2P: R.K.O.SIGEL,D.G.SASHITAL,D.L.ABRAMOVITZ,A.G.PALMER III, S.E.BUTCHER,A.M.PYLE |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.9 KB | Display | ![]() |
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PDB format | ![]() | 90.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 322.9 KB | Display | ![]() |
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Full document | ![]() | 352.5 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: RNA chain | Mass: 10970.567 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: This is a Molecular Dynamics re-refinement of structures from the PDB: 1R2P ensemble using the NMR restraints. The re-refinement shows significant changes in the overall geometry |
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NMR details | Text: AUTHOR USED THE MR DATA FROM ENTRY 1R2P. |
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Processing
NMR software | Name: ![]() Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman Classification: refinement |
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Refinement | Method: molecular dynamics / Software ordinal: 1 |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 5 / Conformers submitted total number: 5 |