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

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General features for molecule PDB_00847
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00847
Molecule name [?]:CRYSTAL STRUCTURE OF VIRGINIAMYCIN M AND S BOUND TO THE 50S RIBOSOMAL SUBUNIT OF HALOARCULA MARISMOR
Source [?]:RCSB Protein Data Bank
Source ID [?]:1YIT
Reference [?]:D.TU,G.BLAHA,P.B.MOORE,T.A.STEITZ. STRUCTURES OF MLSBK ANTIBIOTICS BOUND TO MUTATED LARGE RIBOSOMAL SUBUNITS PROVIDE A STRUCTURAL EXPLANATION FOR RESISTANCE.. CELL V. 121 257 2005 ISSN 0092-8674
Type [?]:23S Ribosomal RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:HALOARCULA MARISMORTUI
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 2.80 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:2876
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00848
Number of domains [?]:3
Number of unpaired bases [?]:940
Number of paired bases [?]:1936

Click on any header below for additional features.

Stem features

Number of stems [?]:144
Number of base pairs in stems [?]:734
Maximum length of a stem [?]:13
Average length of a stem [?]:5.1
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-7.36
Minimum estimated free energy [?]:-21.2

Hairpin loop features

Number of hairpin loops [?]:59
Maximum number of free bases in hairpin loops [?]:9
Average number of free bases in hairpin loops [?]:4.19
Minimum number of free bases in hairpin loop [?]:1

Bulge loop features
Number of bulge loops [?]:43
Maximum number of free bases in bulge loops [?]:4
Average number of free bases in bulge loops [?]:0.76
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:27
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:3
Average internal loop absolute asymmetry:1.11
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 [?]:15
Maximum number of free bases in multi-loops:15
Average number of free bases in multi-loops:2.98
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:15
Average multi-loop absolute asymmetry:2.94
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:15
Average multi-loop relative asymmetry:1.12
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:5
Average number of branches in multi-loops:3.8
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 132
Total number of AA non-canonical base pairs:18
Total number of AC non-canonical base pairs:15
Total number of AG non-canonical base pairs:67
Total number of CC non-canonical base pairs:13
Total number of CU non-canonical base pairs:8
Total number of GG non-canonical base pairs:1
Total number of UU non-canonical base pairs:10

Pseudoknot features
Number of pseudoknots [?]:6
Number of bands:22
Number of base pairs in bands:234
Maximum band length:37
Average band length:10.64
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:233
Average number of unpaired bases:53.5
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:27
Maximum number of base pairs to remove, per pseudoknot:10
Average number of base pairs to remove, per pseudoknot:4.5
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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