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

General features for molecule PDB_00987 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00987 Molecule name [?]: SOLUTION RNA STRUCTURE OF LOOP REGION OF THE HIV-1 DIMERIZATION INITIATION SITE IN THE EXTENDED-DUPL Source [?]: RCSB Protein Data Bank Source ID [?]: 2D18 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 [?]: 34 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00988 Number of domains [?]: 1 Number of unpaired bases [?]: 2 Number of paired bases [?]: 32

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 16 Maximum length of a stem [?]: 6 Average length of a stem [?]: 5.33 Minimum length of a stem [?]: 5 Maximum estimated free energy [?]: -6.9 Average estimated free energy [?]: -8.6 Minimum estimated free energy [?]: -12

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 [?]: 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 AA non-canonical base pairs: 2

Pseudoknot features