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

General features for molecule PDB_01156 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01156 Molecule name [?]: CRYSTAL STRUCTURE OF AN RNA DOMAIN FROM HEPATITIS C VIRUS. Source [?]: RCSB Protein Data Bank Source ID [?]: 2NOK Reference [?]: S.M.DIBROV,H.JOHNSTON-COX,Y.H.WENG,T.HERMANN. FUNCTIONAL ARCHITECTURE OF HCV IRES DOMAIN II STABILIZED BY DIVALENT METAL IONS IN THE CRYSTAL AND IN SOLUTION.. ANGEW.CHEM.INT.ED.ENGL. V. 46 226 2007 ASTM ACIEAY GE ISSN 0570-0833 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 3.00 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 88 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 2 Number of unpaired bases [?]: 18 Number of paired bases [?]: 70

Click on any header below for additional features.

Stem features Number of stems [?]: 7 Number of base pairs in stems [?]: 35 Maximum length of a stem [?]: 8 Average length of a stem [?]: 5 Minimum length of a stem [?]: 3 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.04 Minimum estimated free energy [?]: -13.5

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 1 Average number of free bases in hairpin loops [?]: 1 Minimum number of free bases in hairpin loop [?]: 1

Bulge loop features Number of bulge loops [?]: 4 Maximum number of free bases in bulge loops [?]: 5 Average number of free bases in bulge loops [?]: 1.5 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 1 Maximum number of free bases in internal loops: 1 Average number of free bases in internal loops: 1 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 0 Average internal loop absolute asymmetry: 0 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 1 Average internal loop relative asymmetry: 1 Minimum internal loop relative asymmetry: 1

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 4 Total number of CU non-canonical base pairs: 2 Total number of UU non-canonical base pairs: 2

Pseudoknot features