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

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General features for molecule PDB_00795
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00795
Molecule name [?]:CRYSTAL STRUCTURE OF A 70S RIBOSOME-TRNA COMPLEX REVEALS FUNCTIONAL INTERACTIONS AND REARRANGEMENTS.
Source [?]:RCSB Protein Data Bank
Source ID [?]:1VSA
Reference [?]:A.KOROSTELEV,S.TRAKHANOV,M.LAURBERG,H.F.NOLLER. CRYSTAL STRUCTURE OF A 70S RIBOSOME-TRNA COMPLEX REVEALS FUNCTIONAL INTERACTIONS AND REARRANGEMENTS. CELL(CAMBRIDGE,MASS.) V. 126 1065 2006 ASTM CELLB5 US ISSN 0092-8674
Type [?]:23S 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 3.71 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:3009
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00796
Number of domains [?]:2
Number of unpaired bases [?]:1021
Number of paired bases [?]:1988

Click on any header below for additional features.

Stem features

Number of stems [?]:148
Number of base pairs in stems [?]:761
Maximum length of a stem [?]:18
Average length of a stem [?]:5.14
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-8.69
Minimum estimated free energy [?]:-33.6

Hairpin loop features

Number of hairpin loops [?]:59
Maximum number of free bases in hairpin loops [?]:13
Average number of free bases in hairpin loops [?]:4.68
Minimum number of free bases in hairpin loop [?]:1

Bulge loop features
Number of bulge loops [?]:39
Maximum number of free bases in bulge loops [?]:9
Average number of free bases in bulge loops [?]:0.9
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:34
Maximum number of free bases in internal loops:11
Average number of free bases in internal loops:2.12
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:10
Average internal loop absolute asymmetry:0.94
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:11
Average internal loop relative asymmetry:1.68
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:16
Maximum number of free bases in multi-loops:20
Average number of free bases in multi-loops:3.07
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:20
Average multi-loop absolute asymmetry:3.32
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:20
Average multi-loop relative asymmetry:1.3
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:5
Average number of branches in multi-loops:3.75
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 114
Total number of AA non-canonical base pairs:16
Total number of AC non-canonical base pairs:6
Total number of AG non-canonical base pairs:79
Total number of CC non-canonical base pairs:1
Total number of CU non-canonical base pairs:3
Total number of GG non-canonical base pairs:3
Total number of UU non-canonical base pairs:6

Pseudoknot features
Number of pseudoknots [?]:6
Number of bands:22
Number of base pairs in bands:233
Maximum band length:43
Average band length:10.59
Minimum band length:2
Maximum number of bands per pseudoknot:9
Average number of bands per pseudoknot:3.67
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:7
Average number of un-bands:1.33
Minimum number of un-bands:0
Maximum number of in-bands:24
Average number of in-bands:4.5
Minimum number of in-bands:0
Maximum number of unpaired bases:267
Average number of unpaired bases:57.83
Minimum number of unpaired bases:8
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:26
Maximum number of base pairs to remove, per pseudoknot:9
Average number of base pairs to remove, per pseudoknot:4.33
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:9
Maximum number of bands to remove, per pseudoknot:3
Average number of bands to remove, per pseudoknot:1.5
Minimum number of bands to remove, per pseudoknot:1



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