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

General features for molecule PDB_01260 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01260 Molecule name [?]: SUBSTRATE RNA POSITIONING IN THE ARCHAEAL H/ACA RIBONUCLEOPROTEIN COMPLEX Source [?]: RCSB Protein Data Bank Source ID [?]: 2RFK Reference [?]: B.LIANG,S.XUE,R.M.TERNS,M.P.TERNS,H.LI. SUBSTRATE RNA POSITIONING IN THE ARCHAEAL H/ACA RIBONUCLEOPROTEIN COMPLEX.. NAT.STRUCT.MOL.BIOL. 2007 US ESSN 1545-9985 Type [?]: Transfer RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: PYROCOCCUS FURIOSUS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.87 ANGSTROMS; ran through RNAview Number of molecules [?]: 3 Length [?]: 61 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 11 Number of paired bases [?]: 50

Click on any header below for additional features.

Stem features Number of stems [?]: 1 Number of base pairs in stems [?]: 5 Maximum length of a stem [?]: 5 Average length of a stem [?]: 5 Minimum length of a stem [?]: 5 Maximum estimated free energy [?]: -11.3 Average estimated free energy [?]: -11.3 Minimum estimated free energy [?]: -11.3

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 0 Average number of free bases in hairpin loops [?]: 0 Minimum number of free bases in hairpin loop [?]: 0

Bulge loop features Number of bulge loops [?]: 0 Maximum number of free bases in bulge loops [?]: N/A Average number of free bases in bulge loops [?]: N/A Minimum number of free bases in bulge loop [?]: N/A

Internal loop features

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 0

Pseudoknot features Number of pseudoknots [?]: 1 Number of bands: 2 Number of base pairs in bands: 20 Maximum band length: 11 Average band length: 10 Minimum band length: 9 Maximum number of bands per pseudoknot: 2 Average number of bands per pseudoknot: 2 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 0 Average number of un-bands: 0 Minimum number of un-bands: 0 Maximum number of in-bands: 1 Average number of in-bands: 1 Minimum number of in-bands: 1 Maximum number of unpaired bases: 10 Average number of unpaired bases: 10 Minimum number of unpaired bases: 10 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 9 Maximum number of base pairs to remove, per pseudoknot: 9 Average number of base pairs to remove, per pseudoknot: 9 Minimum number of base pairs to remove, per pseudoknot: 9 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

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