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

General features for molecule PDB_00703 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00703 Molecule name [?]: STRUCTURE OF THE RIBOSOMAL 80S-EEF2-SORDARIN COMPLEX FROM YEAST OBTAINED BY DOCKING ATOMIC MODELS FO Source [?]: RCSB Protein Data Bank Source ID [?]: 1S1H Reference [?]: C.M.SPAHN,M.G.GOMEZ-LORENZO,R.A.GRASSUCCI, R.JORGENSEN,G.R.ANDERSEN,R.BECKMANN,P.A.PENCZEK, J.P.BALLESTA,J.FRANK. DOMAIN MOVEMENTS OF ELONGATION FACTOR EEF2 AND THE EUKARYOTIC 80S RIBOSOME FACILITATE TRNA TRANSLOCATION.. EMBO J. V. 23 1008 2004 ASTM EMJODG UK ISSN 0261-4189 Type [?]: 16S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: SACCHAROMYCES CEREVISIAE Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION11.70 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 1466 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 476 Number of paired bases [?]: 990

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Stem features Number of stems [?]: 92 Number of base pairs in stems [?]: 469 Maximum length of a stem [?]: 15 Average length of a stem [?]: 5.11 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.29 Minimum estimated free energy [?]: -30.7

Hairpin loop features Number of hairpin loops [?]: 28 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.07 Minimum number of free bases in hairpin loop [?]: 1 Total number of UUCG hairpin motifs per molecule [?]: 1

Bulge loop features Number of bulge loops [?]: 30 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.73 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 19 Maximum number of free bases in internal loops: 9 Average number of free bases in internal loops: 2.53 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 0.95 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.53 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 14 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 2.76 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.54 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 7 Average multi-loop relative asymmetry: 1.06 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.5 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 71 Total number of AA non-canonical base pairs: 10 Total number of AC non-canonical base pairs: 10 Total number of AG non-canonical base pairs: 39 Total number of CU non-canonical base pairs: 2 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 7

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 6 Number of base pairs in bands: 26 Maximum band length: 8 Average band length: 4.33 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: 1.67 Minimum number of un-bands: 0 Maximum number of in-bands: 1 Average number of in-bands: 0.33 Minimum number of in-bands: 0 Maximum number of unpaired bases: 27 Average number of unpaired bases: 22.33 Minimum number of unpaired bases: 16 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 7 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 2.33 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 3 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