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

General features for molecule PDB_00813 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00813 Molecule name [?]: STRUCTURE OF AN INOSINE-ADENINE WOBBLE BASE PAIR COMPLEX IN THE CONTEXT OF THE DECODING CENTER Source [?]: RCSB Protein Data Bank Source ID [?]: 1XNQ Reference [?]: F.V.MURPHY,V.RAMAKRISHNAN. STRUCTURE OF A PURINE-PURINE WOBBLE BASE PAIR IN THE DECODING CENTER OF THE RIBOSOME.. NAT.STRUCT.MOL.BIOL. V. 11 1251 2004 US ISSN 1545-9993 Type [?]: 16S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: THERMUS THERMOPHILUS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.05 ANGSTROMS; ran through RNAview Number of molecules [?]: 3 Length [?]: 1522 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 5 Number of unpaired bases [?]: 534 Number of paired bases [?]: 988

Click on any header below for additional features.

Stem features Number of stems [?]: 80 Number of base pairs in stems [?]: 431 Maximum length of a stem [?]: 15 Average length of a stem [?]: 5.4 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.8 Minimum estimated free energy [?]: -30.7

Hairpin loop features Number of hairpin loops [?]: 28 Maximum number of free bases in hairpin loops [?]: 22 Average number of free bases in hairpin loops [?]: 5.46 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 25 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.78 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 16 Maximum number of free bases in internal loops: 14 Average number of free bases in internal loops: 2.72 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 12 Average internal loop absolute asymmetry: 1.69 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 7 Average internal loop relative asymmetry: 1.94 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 10 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 3.03 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.48 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.13 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.2 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 64 Total number of AA non-canonical base pairs: 9 Total number of AC non-canonical base pairs: 7 Total number of AG non-canonical base pairs: 36 Total number of CU non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 63 Maximum band length: 32 Average band length: 7.88 Minimum band length: 2 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: 1.25 Minimum number of un-bands: 0 Maximum number of in-bands: 9 Average number of in-bands: 2.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 75 Average number of unpaired bases: 31.75 Minimum number of unpaired bases: 9 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 11 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.75 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 4 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