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

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General features for molecule PDB_01180
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_01180
Molecule name [?]:1.8 A X-RAY CRYSTAL STRUCTURE OF APRAMYCIN COMPLEX WITH RNA FRAGMENT GGGCGUCGCUAGUACC/CGGUACUAAAAGUC
Source [?]:RCSB Protein Data Bank
Source ID [?]:2OE8
Reference [?]:T.HERMANN,V.TERESHKO,E.SKRIPKIN,D.J.PATEL. APRAMYCIN RECOGNITION BY THE HUMAN RIBOSOMAL DECODING SITE.. BLOOD CELLS MOL.DIS. V. 38 193 2007 US ISSN 1079-9796
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 1.80 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:33
Fragments used [?]:Yes
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_01179
Number of domains [?]:1
Number of unpaired bases [?]:5
Number of paired bases [?]:28

Click on any header below for additional features.

Stem features

Number of stems [?]:2
Number of base pairs in stems [?]:14
Maximum length of a stem [?]:7
Average length of a stem [?]:7
Minimum length of a stem [?]:7
Maximum estimated free energy [?]:-9.1
Average estimated free energy [?]:-10.75
Minimum estimated free energy [?]:-12.4

Hairpin loop features

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

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

Multi-loop features

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

Pseudoknot features



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