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

General features for molecule PDB_01114 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01114 Molecule name [?]: CRYSTAL STRUCTURE OF AN E. COLI THI-BOX RIBOSWITCH BOUND TO THIAMINE MONOPHOSPHATE Source [?]: RCSB Protein Data Bank Source ID [?]: 2HOM Reference [?]: T.E.EDWARDS,A.R.FERRE-D'AMARE. CRYSTAL STRUCTURES OF THE THI-BOX RIBOSWITCH BOUND TO THIAMINE PYROPHOSPHATE ANALOGS REVEAL ADAPTIVE RNA-SMALL MOLECULE RECOGNITION. STRUCTURE V. 14 1459 2006 ASTM STRUE6 UK ISSN 0969-2126 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 2.89 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 76 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 22 Number of paired bases [?]: 54

Click on any header below for additional features.

Stem features Number of stems [?]: 5 Number of base pairs in stems [?]: 27 Maximum length of a stem [?]: 7 Average length of a stem [?]: 5.4 Minimum length of a stem [?]: 4 Maximum estimated free energy [?]: -5.4 Average estimated free energy [?]: -8.22 Minimum estimated free energy [?]: -12.5

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 7 Average number of free bases in hairpin loops [?]: 6.5 Minimum number of free bases in hairpin loop [?]: 6

Bulge loop features Number of bulge loops [?]: 2 Maximum number of free bases in bulge loops [?]: 6 Average number of free bases in bulge loops [?]: 1.75 Minimum number of free bases in bulge loop [?]: 0

Internal loop features

Multi-loop features Number of multi-loops [?]: 1 Maximum number of free bases in multi-loops: 1 Average number of free bases in multi-loops: 0.33 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 1 Average multi-loop absolute asymmetry: 0.67 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 0 Average multi-loop relative asymmetry: 0 Minimum multi-loop relative asymmetry: 0 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 [?]: 6 Total number of AA non-canonical base pairs: 1 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: 1

Pseudoknot features