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

General features for molecule PDB_00989 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00989 Molecule name [?]: SOLUTION RNA STRUCTURE MODEL OF THE HIV-1 DIMERIZATION INITIATION SITE IN THE EXTENDED-DUPLEX DIMER Source [?]: RCSB Protein Data Bank Source ID [?]: 2D1A Reference [?]: S.BABA,K.TAKAHASHI,S.NOGUCHI,H.TAKAKU,Y.KOYANAGI, N.YAMAMOTO,G.KAWAI. SOLUTION RNA STRUCTURES OF THE HIV-1 DIMERIZATION INITIATION SITE IN THE KISSING-LOOP AND EXTENDED-DUPLEX DIMERS.. J.BIOCHEM.(TOKYO) V. 138 583 2005 ASTM JOBIAO JA ISSN 0021-924X 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 [?]: 2 Length [?]: 78 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00990 Number of domains [?]: 1 Number of unpaired bases [?]: 6 Number of paired bases [?]: 72

Click on any header below for additional features.

Stem features Number of stems [?]: 5 Number of base pairs in stems [?]: 36 Maximum length of a stem [?]: 9 Average length of a stem [?]: 7.2 Minimum length of a stem [?]: 6 Maximum estimated free energy [?]: -12 Average estimated free energy [?]: -12.64 Minimum estimated free energy [?]: -13.6

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 0 Average number of free bases in hairpin loops [?]: 0 Minimum number of free bases in hairpin loop [?]: 0

Bulge loop features Number of bulge loops [?]: 4 Maximum number of free bases in bulge loops [?]: 2 Average number of free bases in bulge loops [?]: 0.75 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 [?]: 4 Total number of AA non-canonical base pairs: 2 Total number of AG non-canonical base pairs: 2

Pseudoknot features