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

General features for molecule PDB_00917 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00917 Molecule name [?]: CRYSTAL STRUCTURE OF THE RNA SUBUNIT OF RIBONUCLEASE P. BACTERIAL A-TYPE. Source [?]: RCSB Protein Data Bank Source ID [?]: 2A2E Reference [?]: A.TORRES-LARIOS,K.K.SWINGER,A.S.KRASILNIKOV,T.PAN, A.MONDRAGON. CRYSTAL STRUCTURE OF THE RNA COMPONENT OF BACTERIAL RIBONUCLEASE P.. NATURE V. 437 584 2005 ASTM NATUAS UK ISSN 1476-4687 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 3.85 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 266 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 76 Number of paired bases [?]: 190

Click on any header below for additional features.

Stem features Number of stems [?]: 15 Number of base pairs in stems [?]: 60 Maximum length of a stem [?]: 10 Average length of a stem [?]: 4 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.73 Minimum estimated free energy [?]: -23.5

Hairpin loop features Number of hairpin loops [?]: 7 Maximum number of free bases in hairpin loops [?]: 11 Average number of free bases in hairpin loops [?]: 3.43 Minimum number of free bases in hairpin loop [?]: 0

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 [?]: 1.25 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 4 Maximum number of free bases in internal loops: 3 Average number of free bases in internal loops: 1.62 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 0.75 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.75 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 2 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 2.88 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 9 Average multi-loop absolute asymmetry: 2.92 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 10 Average multi-loop relative asymmetry: 1.38 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 4 Minimum number of branches in multi-loops: 4

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 3 Total number of AG non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 1

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 5 Number of base pairs in bands: 35 Maximum band length: 13 Average band length: 7 Minimum band length: 4 Maximum number of bands per pseudoknot: 3 Average number of bands per pseudoknot: 2.5 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 3 Average number of un-bands: 2 Minimum number of un-bands: 1 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 7 Average number of unpaired bases: 5.5 Minimum number of unpaired bases: 4 Several ways to remove minimum number of base pairs, per molecule: Yes Minimum number of base pairs to remove, per molecule: 11 Maximum number of base pairs to remove, per pseudoknot: 7 Average number of base pairs to remove, per pseudoknot: 5.5 Minimum number of base pairs to remove, per pseudoknot: 4 Minimum number of bands to remove, per molecule: 2 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