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

General features for molecule PDB_00039 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00039 Molecule name [?]: CRYSTAL STRUCTURE OF THE REV BINDING ELEMENT OF HIV-1 Source [?]: RCSB Protein Data Bank Source ID [?]: 1DUQ Reference [?]: L.W.HUNG,E.L.HOLBROOK,S.R.HOLBROOK. THE CRYSTAL STRUCTURE OF THE REV BINDING ELEMENT OF HIV-1 REVEALS NOVEL BASE PAIRING AND CONFORMATIONAL VARIABILITY.. PROC.NATL.ACAD.SCI.USA V. 97 5107 2000 ASTM PNASA6 US ISSN 0027-8424 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 [?]: X-RAY, RESOLUTION 2.10 ANGSTROMS; ran through RNAview Number of molecules [?]: 8 Length [?]: 104 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 14 Number of paired bases [?]: 90

Click on any header below for additional features.

Stem features Number of stems [?]: 12 Number of base pairs in stems [?]: 45 Maximum length of a stem [?]: 5 Average length of a stem [?]: 3.75 Minimum length of a stem [?]: 3 Maximum estimated free energy [?]: -2.4 Average estimated free energy [?]: -5.55 Minimum estimated free energy [?]: -7.6

Hairpin loop features Number of hairpin loops [?]: 4 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 [?]: 6 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 Number of internal loops [?]: 2 Maximum number of free bases in internal loops: 2 Average number of free bases in internal loops: 1.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 1 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 2

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 6 Total number of AG non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 4

Pseudoknot features

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