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

General features for molecule PDB_01117 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01117 Molecule name [?]: SOLUTION STRUCTURE OF CSFV IRES DOMAIN IIA Source [?]: RCSB Protein Data Bank Source ID [?]: 2HUA Reference [?]: N.LOCKER,L.E.EASTON,P.J.LUKAVSKY. HCV AND CSFV IRES DOMAIN II MEDIATE EIF2 RELEASE DURING 80S RIBOSOME ASSEMBLY.. EMBO J. V. 26 795 2007 ASTM EMJODG UK ISSN 0261-4189 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 [?]: 40 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 6 Number of paired bases [?]: 34

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 17 Maximum length of a stem [?]: 8 Average length of a stem [?]: 5.67 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -3.4 Average estimated free energy [?]: -8.87 Minimum estimated free energy [?]: -17.8

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

Bulge loop features Number of bulge loops [?]: 2 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 1 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 [?]: 3 Total number of AC non-canonical base pairs: 1 Total number of AG non-canonical base pairs: 2

Pseudoknot features