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

General features for molecule PDB_00908 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00908 Molecule name [?]: CRYSTAL STRUCTURE OF A GROUP I INTRON/TWO EXON COMPLEX THAT INCLUDES ALL CATALYTIC METAL ION LIGANDS Source [?]: RCSB Protein Data Bank Source ID [?]: 1ZZN Reference [?]: M.R.STAHLEY,S.A.STROBEL. STRUCTURAL EVIDENCE FOR A TWO-METAL-ION MECHANISM OF GROUP I INTRON SPLICING.. SCIENCE V. 309 1587 2005 ASTM SCIEAS US ISSN 0036-8075 Type [?]: Group I Intron [?]     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 3.37 ANGSTROMS; ran through RNAview Number of molecules [?]: 3 Length [?]: 222 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00747 Number of domains [?]: 1 Number of unpaired bases [?]: 72 Number of paired bases [?]: 150

Click on any header below for additional features.

Stem features Number of stems [?]: 11 Number of base pairs in stems [?]: 55 Maximum length of a stem [?]: 8 Average length of a stem [?]: 5 Minimum length of a stem [?]: 3 Maximum estimated free energy [?]: -3.3 Average estimated free energy [?]: -8.25 Minimum estimated free energy [?]: -14.9

Hairpin loop features Number of hairpin loops [?]: 5 Maximum number of free bases in hairpin loops [?]: 16 Average number of free bases in hairpin loops [?]: 5.6 Minimum number of free bases in hairpin loop [?]: 2

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 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: 2.12 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 0.75 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 1.25 Minimum internal loop relative asymmetry: 1

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 10 Total number of AA non-canonical base pairs: 3 Total number of AC non-canonical base pairs: 2 Total number of AG non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 1

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 4 Number of base pairs in bands: 20 Maximum band length: 6 Average band length: 5 Minimum band length: 3 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: 3 Average number of un-bands: 3 Minimum number of un-bands: 3 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 18 Average number of unpaired bases: 11.5 Minimum number of unpaired bases: 5 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 8 Maximum number of base pairs to remove, per pseudoknot: 5 Average number of base pairs to remove, per pseudoknot: 4 Minimum number of base pairs to remove, per pseudoknot: 3 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

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