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

General features for molecule PDB_01159 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01159 Molecule name [?]: CRYSTAL STRUCTURE OF JUNCTIONED HAIRPIN RIBOZYME INCORPORATING SYNTHETIC PROPYL LINKER Source [?]: RCSB Protein Data Bank Source ID [?]: 2NPZ Reference [?]: C.MACELREVEY,R.C.SPITALE,J.KRUCINSKA,J.E.WEDEKIND. A POSTERIORI DESIGN OF CRYSTAL CONTACTS TO IMPROVE THE X-RAY DIFFRACTION PROPERTIES OF A SMALL RNA ENZYME.. ACTA CRYSTALLOGR.,SECT.D V. 63 812 2007 ASTM ABCRE6 DK ISSN 0907-4449 Type [?]: Hairpin Ribozyme [?]     PS figure     PDF figure Figure from original source Organism [?]: N/A Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.35 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 61 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00806, PDB_00956, PDB_01052, PDB_01197, PDB_01200 Number of domains [?]: 2 Number of unpaired bases [?]: 21 Number of paired bases [?]: 40

Click on any header below for additional features.

Stem features Number of stems [?]: 4 Number of base pairs in stems [?]: 20 Maximum length of a stem [?]: 7 Average length of a stem [?]: 5 Minimum length of a stem [?]: 3 Maximum estimated free energy [?]: -6.6 Average estimated free energy [?]: -8.63 Minimum estimated free energy [?]: -10.9

Hairpin loop features Number of hairpin loops [?]: 2 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 Number of internal loops [?]: 2 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 5 Minimum number of free bases in internal loop: 4 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 1 Average internal loop relative asymmetry: 1 Minimum internal loop relative asymmetry: 1

Multi-loop features

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

Pseudoknot features

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