RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database

General features for molecule PDB_00743 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00743 Molecule name [?]: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN WT BACTERIOPHAGE MS2 COAT PROTEIN AND AN F5 APTAMER RNA STEML Source [?]: RCSB Protein Data Bank Source ID [?]: 1U1Y Reference [?]: W.T.HORN,M.A.CONVERY,N.J.STONEHOUSE,C.J.ADAMS, L.LILJAS,S.E.PHILLIPS,P.G.STOCKLEY. THE CRYSTAL STRUCTURE OF A HIGH AFFINITY RNA STEM-LOOP COMPLEXED WITH THE BACTERIOPHAGE MS2 CAPSID: FURTHER CHALLENGES IN THE MODELING OF LIGAND-RNA INTERACTIONS.. RNA V. 10 1776 2004 ASTM RNARFU UK ISSN 1355-8382 Type [?]: Viral & Phage RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: BACTERIOPHAGE MS2 Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.85 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 33 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 2 Number of unpaired bases [?]: 11 Number of paired bases [?]: 22

Click on any header below for additional features.

Stem features Number of stems [?]: 4 Number of base pairs in stems [?]: 11 Maximum length of a stem [?]: 4 Average length of a stem [?]: 2.75 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: -2.4 Average estimated free energy [?]: -3.67 Minimum estimated free energy [?]: -5.7

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 4 Average number of free bases in hairpin loops [?]: 4 Minimum number of free bases in hairpin loop [?]: 4

Bulge loop features Number of bulge loops [?]: 2 Maximum number of free bases in bulge loops [?]: 1 Average number of free bases in bulge loops [?]: 0.5 Minimum number of free bases in bulge loop [?]: 0

Internal loop features

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 2 Total number of AG non-canonical base pairs: 2

Pseudoknot features