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

General features for molecule PDB_00557 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00557 Molecule name [?]: TRANSITION STATE STABILIZATION BY A CATALYTIC RNA Source [?]: RCSB Protein Data Bank Source ID [?]: 1M5O Reference [?]: P.B.RUPERT,A.P.MASSEY,S.T.SIGURDSSON, A.R.FERRE-D'AMARE. TRANSITION STATE STABILIZATION BY A CATALYTIC RNA. SCIENCE V. 298 1421 2002 ASTM SCIEAS US ISSN 0036-8075 Type [?]: Synthetic RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: HOMO SAPIENS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.20 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 226 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00555, PDB_00558, PDB_00559 Number of domains [?]: 2 Number of unpaired bases [?]: 50 Number of paired bases [?]: 176

Click on any header below for additional features.

Stem features Number of stems [?]: 14 Number of base pairs in stems [?]: 88 Maximum length of a stem [?]: 10 Average length of a stem [?]: 6.29 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -10.24 Minimum estimated free energy [?]: -19.4

Hairpin loop features Number of hairpin loops [?]: 6 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4 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 [?]: 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: 2.25 Minimum number of free bases in internal loop: 2 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 0.5 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 Number of multi-loops [?]: 2 Maximum number of free bases in multi-loops: 1 Average number of free bases in multi-loops: 0.25 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 1 Average multi-loop absolute asymmetry: 0.34 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 1 Average multi-loop relative asymmetry: 0.17 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 [?]: 12 Total number of AA non-canonical base pairs: 2 Total number of AC non-canonical base pairs: 4 Total number of AG non-canonical base pairs: 6

Pseudoknot features

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