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

General features for molecule PDB_01070 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01070 Molecule name [?]: CRYSTAL STRUCTURE OF THIAMINE PYROPHOSPHATE-SPECIFIC RIBOSWITCH IN COMPLEX WITH THIAMINE PYROPHOSPHA Source [?]: RCSB Protein Data Bank Source ID [?]: 2GDI Reference [?]: A.SERGANOV,A.POLONSKAIA,A.T.PHAN,R.R.BREAKER, D.J.PATEL. STRUCTURAL BASIS FOR GENE REGULATION BY A THIAMINE PYROPHOSPHATE-SENSING RIBOSWITCH.. NATURE V. 441 1167 2006 ASTM NATUAS UK ISSN 0028-0836 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 2.05 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 160 Fragments used [?]: Yes Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 52 Number of paired bases [?]: 108

Click on any header below for additional features.

Stem features Number of stems [?]: 6 Number of base pairs in stems [?]: 20 Maximum length of a stem [?]: 4 Average length of a stem [?]: 3.33 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -4.3 Minimum estimated free energy [?]: -7.5

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

Bulge loop features Number of bulge loops [?]: 4 Maximum number of free bases in bulge loops [?]: 1 Average number of free bases in bulge loops [?]: 0.5 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 [?]: 6 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: 2

Pseudoknot features Number of pseudoknots [?]: 1 Number of bands: 3 Number of base pairs in bands: 34 Maximum band length: 16 Average band length: 11.33 Minimum band length: 2 Maximum number of bands per pseudoknot: 3 Average number of bands per pseudoknot: 3 Minimum number of bands per pseudoknot: 3 Maximum number of un-bands: 0 Average number of un-bands: 0 Minimum number of un-bands: 0 Maximum number of in-bands: 2 Average number of in-bands: 2 Minimum number of in-bands: 2 Maximum number of unpaired bases: 36 Average number of unpaired bases: 36 Minimum number of unpaired bases: 36 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 2 Maximum number of base pairs to remove, per pseudoknot: 2 Average number of base pairs to remove, per pseudoknot: 2 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 1 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