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

General features for molecule PDB_01261 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01261 Molecule name [?]: COCRYSTAL STRUCTURE OF A TYROSYL-TRNA SYNTHETASE SPLICING FACTOR WITH A GROUP I INTRON RNA Source [?]: RCSB Protein Data Bank Source ID [?]: 2RKJ Reference [?]: P.J.PAUKSTELIS,J.H.CHEN,E.CHASE,A.M.LAMBOWITZ, B.L.GOLDEN. STRUCTURE OF A TYROSYL-TRNA SYNTHETASE SPLICING FACTOR BOUND TO A GROUP I INTRON RNA.. NATURE V. 451 94 2008 ASTM NATUAS UK ISSN 0028-0836 Type [?]: Other RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: STAPHYLOCOCCUS PHAGE TWORT Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 4.50 ANGSTROMS; ran through RNAview Number of molecules [?]: 8 Length [?]: 968 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 3 Number of unpaired bases [?]: 296 Number of paired bases [?]: 672

Click on any header below for additional features.

Stem features Number of stems [?]: 48 Number of base pairs in stems [?]: 278 Maximum length of a stem [?]: 10 Average length of a stem [?]: 5.79 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: -0.9 Average estimated free energy [?]: -7.87 Minimum estimated free energy [?]: -14.5

Hairpin loop features Number of hairpin loops [?]: 30 Maximum number of free bases in hairpin loops [?]: 7 Average number of free bases in hairpin loops [?]: 3.07 Minimum number of free bases in hairpin loop [?]: 0

Bulge loop features Number of bulge loops [?]: 8 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 Number of internal loops [?]: 4 Maximum number of free bases in internal loops: 3 Average number of free bases in internal loops: 2 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 2 Minimum internal loop absolute asymmetry: 2 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 3 Minimum internal loop relative asymmetry: 3

Multi-loop features Number of multi-loops [?]: 6 Maximum number of free bases in multi-loops: 9 Average number of free bases in multi-loops: 3.5 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 3.84 Minimum multi-loop absolute asymmetry: 1 Maximum multi-loop relative asymmetry: 4.5 Average multi-loop relative asymmetry: 1.48 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.33 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 46 Total number of AA non-canonical base pairs: 16 Total number of AG non-canonical base pairs: 18 Total number of CC non-canonical base pairs: 4 Total number of CU non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 4

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 13 Number of base pairs in bands: 58 Maximum band length: 6 Average band length: 4.46 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 4.33 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 12 Average number of un-bands: 7.33 Minimum number of un-bands: 5 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 64 Average number of unpaired bases: 36.67 Minimum number of unpaired bases: 23 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: 10 Average number of base pairs to remove, per pseudoknot: 6 Minimum number of base pairs to remove, per pseudoknot: 4 Minimum number of bands to remove, per molecule: 5 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.67 Minimum number of bands to remove, per pseudoknot: 1