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

General features for molecule PDB_00986 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00986 Molecule name [?]: SOLUTION RNA STRUCTURE OF STEM-BULGE-STEM REGION OF THE HIV- 1 DIMERIZATION INITIATION SITE Source [?]: RCSB Protein Data Bank Source ID [?]: 2D17 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 [?]: 30 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 2 Number of paired bases [?]: 28

Click on any header below for additional features.

Stem features Number of stems [?]: 2 Number of base pairs in stems [?]: 14 Maximum length of a stem [?]: 8 Average length of a stem [?]: 7 Minimum length of a stem [?]: 6 Maximum estimated free energy [?]: -12 Average estimated free energy [?]: -12.8 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 [?]: 1 Maximum number of free bases in bulge loops [?]: 2 Average number of free bases in bulge loops [?]: 1 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 AG non-canonical base pairs: 1

Pseudoknot features