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

General features for molecule PDB_00979 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00979 Molecule name [?]: STRUCTURE OF THE ARABIDOPSIS THALIANA THIAMINE PYROPHOSPHATE RIBOSWITCH WITH ITS REGULATORY LIGAND Source [?]: RCSB Protein Data Bank Source ID [?]: 2CKY Reference [?]: S.THORE,M.LEIBUNDGUT,N.BAN. STRUCTURE OF THE EUKARYOTIC THIAMINE PYROPHOSPHATE RIBOSWITCH WITH ITS REGULATORY LIGAND.. SCIENCE V. 312 1208 2006 ASTM SCIEAS US ISSN 0036-8075 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 2.90 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 154 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 2 Number of unpaired bases [?]: 58 Number of paired bases [?]: 96

Click on any header below for additional features.

Stem features Number of stems [?]: 14 Number of base pairs in stems [?]: 48 Maximum length of a stem [?]: 5 Average length of a stem [?]: 3.43 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -4.91 Minimum estimated free energy [?]: -8.7

Hairpin loop features Number of hairpin loops [?]: 4 Maximum number of free bases in hairpin loops [?]: 6 Average number of free bases in hairpin loops [?]: 5 Minimum number of free bases in hairpin loop [?]: 4

Bulge loop features Number of bulge loops [?]: 8 Maximum number of free bases in bulge loops [?]: 6 Average number of free bases in bulge loops [?]: 1.12 Minimum number of free bases in bulge loop [?]: 0

Internal loop features

Multi-loop features Number of multi-loops [?]: 2 Maximum number of free bases in multi-loops: 4 Average number of free bases in multi-loops: 2.67 Minimum number of free bases in multi-loop: 1 Maximum multi-loop absolute asymmetry: 3 Average multi-loop absolute asymmetry: 2 Minimum multi-loop absolute asymmetry: 1 Maximum multi-loop relative asymmetry: 4 Average multi-loop relative asymmetry: 1.61 Minimum multi-loop relative asymmetry: 0.25 Maximum number of branches in multi-loops: 3 Average number of branches in multi-loops: 3 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 8 Total number of AC non-canonical base pairs: 2 Total number of AG non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 4

Pseudoknot features