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

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General features for molecule PDB_00704
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00704
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 [?]:1S1I
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 [?]:23S 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 [?]:2
Length [?]:2916
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:4
Number of unpaired bases [?]:970
Number of paired bases [?]:1946

Click on any header below for additional features.

Stem features

Number of stems [?]:161
Number of base pairs in stems [?]:832
Maximum length of a stem [?]:13
Average length of a stem [?]:5.17
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-7.6
Minimum estimated free energy [?]:-25.2

Hairpin loop features

Number of hairpin loops [?]:60
Maximum number of free bases in hairpin loops [?]:9
Average number of free bases in hairpin loops [?]:4.23
Minimum number of free bases in hairpin loop [?]:1

Bulge loop features
Number of bulge loops [?]:49
Maximum number of free bases in bulge loops [?]:10
Average number of free bases in bulge loops [?]:1.01
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:30
Maximum number of free bases in internal loops:6
Average number of free bases in internal loops:2.33
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:4
Average internal loop absolute asymmetry:1.13
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.7
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:22
Maximum number of free bases in multi-loops:16
Average number of free bases in multi-loops:2.82
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:15
Average multi-loop absolute asymmetry:2.81
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:16
Average multi-loop relative asymmetry:1.19
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:5
Average number of branches in multi-loops:3.59
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 150
Total number of AA non-canonical base pairs:18
Total number of AC non-canonical base pairs:18
Total number of AG non-canonical base pairs:79
Total number of CC non-canonical base pairs:13
Total number of CU non-canonical base pairs:10
Total number of GG non-canonical base pairs:1
Total number of UU non-canonical base pairs:11

Pseudoknot features
Number of pseudoknots [?]:7
Number of bands:16
Number of base pairs in bands:141
Maximum band length:37
Average band length:8.81
Minimum band length:2
Maximum number of bands per pseudoknot:3
Average number of bands per pseudoknot:2.29
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:5
Average number of un-bands:1.29
Minimum number of un-bands:0
Maximum number of in-bands:16
Average number of in-bands:2.71
Minimum number of in-bands:0
Maximum number of unpaired bases:150
Average number of unpaired bases:34.29
Minimum number of unpaired bases:3
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:23
Maximum number of base pairs to remove, per pseudoknot:6
Average number of base pairs to remove, per pseudoknot:3.29
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:7
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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