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

General features for molecule PDB_00884 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00884 Molecule name [?]: SOLUTION STRUCTURE OF BIV TAR HAIRPIN COMPLEXED TO JDV TAT ARGININE-RICH MOTIF Source [?]: RCSB Protein Data Bank Source ID [?]: 1ZBN Reference [?]: V.CALABRO,M.D.DAUGHERTY,A.D.FRANKEL. A SINGLE INTERMOLECULAR CONTACT MEDIATES INTRAMOLECULAR STABILIZATION OF BOTH RNA AND PROTEIN.. PROC.NATL.ACAD.SCI.USA V. 102 6849 2005 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 [?]: NMR; ran through RNAview Number of molecules [?]: 1 Length [?]: 28 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00317, PDB_00574, PDB_00921 Number of domains [?]: 1 Number of unpaired bases [?]: 10 Number of paired bases [?]: 18

Click on any header below for additional features.

Stem features Number of stems [?]: 2 Number of base pairs in stems [?]: 9 Maximum length of a stem [?]: 5 Average length of a stem [?]: 4.5 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -7.6 Average estimated free energy [?]: -8.95 Minimum estimated free energy [?]: -10.3

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

Bulge loop features Number of bulge loops [?]: 0 Maximum number of free bases in bulge loops [?]: N/A Average number of free bases in bulge loops [?]: N/A Minimum number of free bases in bulge loop [?]: N/A

Internal loop features Number of internal loops [?]: 1 Maximum number of free bases in internal loops: 3 Average number of free bases in internal loops: 2 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 2 Minimum internal loop absolute asymmetry: 2 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 3 Minimum internal loop relative asymmetry: 3

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 0

Pseudoknot features

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