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

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General features for molecule PDB_01200
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_01200
Molecule name [?]:THE NOVEL USE OF A 2',5'-PHOSPHODIESTER LINKAGE AS A REACTION INTERMEDIATE AT THE ACTIVE SITE OF A S
Source [?]:RCSB Protein Data Bank
Source ID [?]:2P7F
Reference [?]:A.T.TORELLI,J.KRUCINSKA,J.E.WEDEKIND. A COMPARISON OF VANADATE TO A 2'-5' LINKAGE AT THE ACTIVE SITE OF A SMALL RIBOZYME SUGGESTS A ROLE FOR WATER IN TRANSITION-STATE STABILIZATION. RNA V. 13 1052 2007 ASTM RNARFU UK ISSN 1355-8382
Type [?]:Other Ribozyme

[?]     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 2.35 ANGSTROMS; ran through RNAview
Number of molecules [?]:4
Length [?]:61
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00806, PDB_00956, PDB_01052, PDB_01159, PDB_01197
Number of domains [?]:2
Number of unpaired bases [?]:11
Number of paired bases [?]:50

Click on any header below for additional features.

Stem features

Number of stems [?]:5
Number of base pairs in stems [?]:25
Maximum length of a stem [?]:7
Average length of a stem [?]:5
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-7.32
Minimum estimated free energy [?]:-10.9

Hairpin loop features

Number of hairpin loops [?]:2
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 [?]:1
Maximum number of free bases in bulge loops [?]:1
Average number of free bases in bulge loops [?]:0.5
Minimum number of free bases in bulge loop [?]:0

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:2.25
Minimum number of free bases in internal loop:2
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:0.5
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:1
Average internal loop relative asymmetry:1
Minimum internal loop relative asymmetry:1

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 5
Total number of AA non-canonical base pairs:1
Total number of AC non-canonical base pairs:2
Total number of AG non-canonical base pairs:2

Pseudoknot features



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