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

General features for molecule PDB_01129 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01129 Molecule name [?]: CRYSTAL STRUCTURE OF PLAUTIA STALI INTESTINE VIRUS INTERGENIC REGION INTERNAL RIBOSOME ENTRY SITE RI Source [?]: RCSB Protein Data Bank Source ID [?]: 2IL9 Reference [?]: J.S.PFINGSTEN,D.A.COSTANTINO,J.S.KIEFT. STRUCTURAL BASIS FOR RIBOSOME RECRUITMENT AND MANIPULATION BY A VIRAL IRES RNA. SCIENCE V. 314 1450 2006 ASTM SCIEAS US ISSN 0036-8075 Type [?]: Internal Ribosome Entry Site [?]     PS figure     PDF figure Figure from original source Organism [?]: PLAUTIA STALI INTESTINE VIRUS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.10 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 267 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 125 Number of paired bases [?]: 142

Click on any header below for additional features.

Stem features Number of stems [?]: 4 Number of base pairs in stems [?]: 14 Maximum length of a stem [?]: 6 Average length of a stem [?]: 3.5 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -3.65 Minimum estimated free energy [?]: -11.2

Hairpin loop features Number of hairpin loops [?]: 4 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 [?]: 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

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 5 Total number of AG non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 1

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 57 Maximum band length: 16 Average band length: 7.12 Minimum band length: 4 Maximum number of bands per pseudoknot: 2 Average number of bands per pseudoknot: 2 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 3 Average number of un-bands: 1.75 Minimum number of un-bands: 0 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 46 Average number of unpaired bases: 28 Minimum number of unpaired bases: 12 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 18 Maximum number of base pairs to remove, per pseudoknot: 6 Average number of base pairs to remove, per pseudoknot: 4.5 Minimum number of base pairs to remove, per pseudoknot: 4 Minimum number of bands to remove, per molecule: 4 Maximum number of bands to remove, per pseudoknot: 1 Average number of bands to remove, per pseudoknot: 1 Minimum number of bands to remove, per pseudoknot: 1