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

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General features for molecule PDB_00719
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00719
Molecule name [?]:COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRIST
Source [?]:RCSB Protein Data Bank
Source ID [?]:1SM1
Reference [?]:J.M.HARMS,F.SCHLUNZEN,P.FUCINI,H.BARTELS,A.YONATH. ALTERATIONS AT THE PEPTIDYL TRANSFERASE CENTRE OF THE RIBOSOME INDUCED BY THE SYNERGISTIC ACTION OF THE STREPTOGRAMINS DALFOPRISTIN AND QUINUPRISTIN.. BMC BIOL. V. 2 4 2004 UK ESSN 1741-7007
Type [?]:23S Ribosomal RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:DEINOCOCCUS RADIODURANS
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 3.42 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:2884
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00609, PDB_00615, PDB_00616, PDB_00808, PDB_00833
Number of domains [?]:2
Number of unpaired bases [?]:1314
Number of paired bases [?]:1570

Click on any header below for additional features.

Stem features

Number of stems [?]:141
Number of base pairs in stems [?]:591
Maximum length of a stem [?]:12
Average length of a stem [?]:4.19
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-6.75
Minimum estimated free energy [?]:-20

Hairpin loop features

Number of hairpin loops [?]:59
Maximum number of free bases in hairpin loops [?]:15
Average number of free bases in hairpin loops [?]:5.95
Minimum number of free bases in hairpin loop [?]:0

Bulge loop features
Number of bulge loops [?]:15
Maximum number of free bases in bulge loops [?]:3
Average number of free bases in bulge loops [?]:0.77
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:51
Maximum number of free bases in internal loops:10
Average number of free bases in internal loops:2.94
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:5
Average internal loop absolute asymmetry:0.94
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.33
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:16
Maximum number of free bases in multi-loops:24
Average number of free bases in multi-loops:3.97
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:21
Average multi-loop absolute asymmetry:4.14
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:20
Average multi-loop relative asymmetry:1.46
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
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 [?]: 51
Total number of AA non-canonical base pairs:6
Total number of AC non-canonical base pairs:6
Total number of AG non-canonical base pairs:29
Total number of CC non-canonical base pairs:2
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:2

Pseudoknot features
Number of pseudoknots [?]:5
Number of bands:18
Number of base pairs in bands:194
Maximum band length:32
Average band length:10.78
Minimum band length:2
Maximum number of bands per pseudoknot:9
Average number of bands per pseudoknot:3.6
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:7
Average number of un-bands:1.8
Minimum number of un-bands:0
Maximum number of in-bands:23
Average number of in-bands:5
Minimum number of in-bands:0
Maximum number of unpaired bases:311
Average number of unpaired bases:80.2
Minimum number of unpaired bases:10
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:22
Maximum number of base pairs to remove, per pseudoknot:10
Average number of base pairs to remove, per pseudoknot:4.4
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:3
Average number of bands to remove, per pseudoknot:1.4
Minimum number of bands to remove, per pseudoknot:1



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