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

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General features for molecule PDB_00652
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00652
Molecule name [?]:CRYSTAL STRUCTURE OF MINIHELIX WITH 3' PUROMYCIN BOUND TO A- SITE OF THE 50S RIBOSOMAL SUBUNIT.
Source [?]:RCSB Protein Data Bank
Source ID [?]:1Q81
Reference [?]:J.L.HANSEN,T.M.SCHMEING,P.B.MOORE,T.A.STEITZ. STRUCTURAL INSIGHTS INTO PEPTIDE BOND FORMATION. PROC.NATL.ACAD.SCI.USA V. 99 11670 2002 ASTM PNASA6 US ISSN 0027-8424
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 2.95 ANGSTROMS; ran through RNAview
Number of molecules [?]:3
Length [?]:2879
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00561, PDB_00653
Number of domains [?]:1
Number of unpaired bases [?]:933
Number of paired bases [?]:1946

Click on any header below for additional features.

Stem features

Number of stems [?]:137
Number of base pairs in stems [?]:720
Maximum length of a stem [?]:13
Average length of a stem [?]:5.26
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-7.58
Minimum estimated free energy [?]:-25.2

Hairpin loop features

Number of hairpin loops [?]:58
Maximum number of free bases in hairpin loops [?]:9
Average number of free bases in hairpin loops [?]:4.17
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 [?]:4
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 [?]:26
Maximum number of free bases in internal loops:6
Average number of free bases in internal loops:2.37
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:4
Average internal loop absolute asymmetry:1.27
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.85
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:14
Maximum number of free bases in multi-loops:15
Average number of free bases in multi-loops:3.04
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:15
Average multi-loop absolute asymmetry:2.91
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:15
Average multi-loop relative asymmetry:1.11
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:5
Average number of branches in multi-loops:3.86
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 135
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:66
Total number of CC non-canonical base pairs:13
Total number of CU non-canonical base pairs:9
Total number of GG non-canonical base pairs:2
Total number of UU non-canonical base pairs:9

Pseudoknot features
Number of pseudoknots [?]:6
Number of bands:25
Number of base pairs in bands:253
Maximum band length:37
Average band length:10.12
Minimum band length:2
Maximum number of bands per pseudoknot:12
Average number of bands per pseudoknot:4.17
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:11
Average number of un-bands:2
Minimum number of un-bands:0
Maximum number of in-bands:22
Average number of in-bands:4.17
Minimum number of in-bands:0
Maximum number of unpaired bases:258
Average number of unpaired bases:57.33
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:29
Maximum number of base pairs to remove, per pseudoknot:12
Average number of base pairs to remove, per pseudoknot:4.83
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:10
Maximum number of bands to remove, per pseudoknot:4
Average number of bands to remove, per pseudoknot:1.67
Minimum number of bands to remove, per pseudoknot:1



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