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

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General features for molecule PDB_01169
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_01169
Molecule name [?]:CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE COMPLEXED WITH PAROMAMINE
Source [?]:RCSB Protein Data Bank
Source ID [?]:2O3V
Reference [?]:J.KONDO,M.HAINRICHSON,I.NUDELMAN,D.SHALLOM-SHEZIFI, C.M.BARBIERI,D.S.PILCH,E.WESTHOF,T.BAASOV. DIFFERENTIAL SELECTIVITY OF NATURAL AND SYNTHETIC AMINOGLYCOSIDES TOWARDS THE EUKARYOTIC AND PROKARYOTIC DECODING A SITES.. CHEMBIOCHEM V. 8 1700 2007 GE ISSN 1439-4227
Type [?]:Other Ribosomal RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:N/A
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 [?]:43
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_01055, PDB_01170, PDB_01172
Number of domains [?]:1
Number of unpaired bases [?]:9
Number of paired bases [?]:34

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:17
Maximum length of a stem [?]:7
Average length of a stem [?]:5.67
Minimum length of a stem [?]:5
Maximum estimated free energy [?]:-5.8
Average estimated free energy [?]:-8.47
Minimum estimated free energy [?]:-13.8

Hairpin loop features

Number of hairpin loops [?]:1
Maximum number of free bases in hairpin loops [?]:0
Average number of free bases in hairpin loops [?]:0
Minimum number of free bases in hairpin loop [?]:0

Bulge loop features
Number of bulge loops [?]:0
Maximum number of free bases in bulge loops [?]:N/A
Average number of free bases in bulge loops [?]:N/A
Minimum number of free bases in bulge loop [?]:N/A

Internal loop features
Number of internal loops [?]:2
Maximum number of free bases in internal loops:3
Average number of free bases in internal loops:2
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:1
Minimum internal loop absolute asymmetry:1
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:1.5
Minimum internal loop relative asymmetry:1

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 3
Total number of AC non-canonical base pairs:1
Total number of UU non-canonical base pairs:2

Pseudoknot features



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