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

General features for molecule PDB_00664 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00664 Molecule name [?]: HIV-1 TAR RNA/NEOMYCIN B COMPLEX Source [?]: RCSB Protein Data Bank Source ID [?]: 1QD3 Reference [?]: C.FABER,H.STICHT,K.SCHWEIMER,P.ROSCH. STRUCTURAL REARRANGEMENTS OF HIV-1 TAT-RESPONSIVE RNA UPON BINDING OF NEOMYCIN B.. J.BIOL.CHEM. V. 275 20660 2000 ASTM JBCHA3 US ISSN 0021-9258 Type [?]: Other RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: NMR; ran through RNAview Number of molecules [?]: 1 Length [?]: 29 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 9 Number of paired bases [?]: 20

Click on any header below for additional features.

Stem features Number of stems [?]: 2 Number of base pairs in stems [?]: 10 Maximum length of a stem [?]: 6 Average length of a stem [?]: 5 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -7.9 Average estimated free energy [?]: -10.6 Minimum estimated free energy [?]: -13.3

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 6 Average number of free bases in hairpin loops [?]: 6 Minimum number of free bases in hairpin loop [?]: 6

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 [?]: 0

Pseudoknot features