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

General features for molecule PDB_00876 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00876 Molecule name [?]: SOLUTION STRUCTURE OF THE HIV-1 FRAMESHIFT INDUCING ELEMENT Source [?]: RCSB Protein Data Bank Source ID [?]: 1Z2J Reference [?]: D.W.STAPLE,S.E.BUTCHER. SOLUTION STRUCTURE AND THERMODYNAMIC INVESTIGATION OF THE HIV-1 FRAMESHIFT INDUCING ELEMENT.. J.MOL.BIOL. V. 349 1011 2005 ASTM JMOBAK UK ISSN 0022-2836 Type [?]: Synthetic RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: SYNTHETIC Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: NMR; ran through RNAview Number of molecules [?]: 1 Length [?]: 45 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 5 Number of paired bases [?]: 40

Click on any header below for additional features.

Stem features Number of stems [?]: 2 Number of base pairs in stems [?]: 20 Maximum length of a stem [?]: 12 Average length of a stem [?]: 10 Minimum length of a stem [?]: 8 Maximum estimated free energy [?]: -15.5 Average estimated free energy [?]: -20.85 Minimum estimated free energy [?]: -26.2

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 2 Average number of free bases in hairpin loops [?]: 2 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 1 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 1.5 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 [?]: 1 Total number of AA non-canonical base pairs: 1

Pseudoknot features