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

General features for molecule PDB_00420 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00420 Molecule name [?]: COMPLEX OF HIV-1 RRE-IIB RNA WITH RSG-1.2 PEPTIDE Source [?]: RCSB Protein Data Bank Source ID [?]: 1G70 Reference [?]: Y.GOSSER,T.HERMANN,A.MAJUMDAR,W.HU,R.FREDERICK, F.JIANG,W.XU,D.J.PATEL. PEPTIDE-TRIGGERED CONFORMATIONAL SWITCH IN HIV-1 RRE RNA COMPLEXES.. NAT.STRUCT.BIOL. V. 8 146 2001 ASTM NSBIEW US ISSN 1072-8368 Type [?]: Other RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: HUMAN IMMUNODEFICIENCY VIRUS 1 Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: NMR; ran through RNAview Number of molecules [?]: 1 Length [?]: 32 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 12 Number of paired bases [?]: 20

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 10 Maximum length of a stem [?]: 4 Average length of a stem [?]: 3.33 Minimum length of a stem [?]: 3 Maximum estimated free energy [?]: -2.4 Average estimated free energy [?]: -3.63 Minimum estimated free energy [?]: -4.3

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 4 Average number of free bases in hairpin loops [?]: 4 Minimum number of free bases in hairpin loop [?]: 4 Total number of UUCG hairpin motifs per molecule [?]: 1

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 AG non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 1

Pseudoknot features