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

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General features for molecule PDB_00136
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00136
Molecule name [?]:CRYSTAL STRUCTURE OF A RNA MOLECULE CONTAINING DOMAIN 5 AND 6 OF THE YEAST AI5G GROUP II SELF-SPLICI
Source [?]:RCSB Protein Data Bank
Source ID [?]:1KXK
Reference [?]:L.ZHANG,J.A.DOUDNA. STRUCTURAL INSIGHTS INTO GROUP II INTRON CATALYSIS AND BRANCH-SITE SELECTION.. SCIENCE V. 295 2084 2002 ASTM SCIEAS US ISSN 0036-8075
Type [?]:Group II Intron

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:YEAST
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 3.00 ANGSTROMS; ran through RNAview
Number of molecules [?]:1
Length [?]:70
Fragments used [?]:Yes
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:18
Number of paired bases [?]:52

Click on any header below for additional features.

Stem features

Number of stems [?]:4
Number of base pairs in stems [?]:26
Maximum length of a stem [?]:10
Average length of a stem [?]:6.5
Minimum length of a stem [?]:5
Maximum estimated free energy [?]:-5.4
Average estimated free energy [?]:-11.4
Minimum estimated free energy [?]:-18.2

Hairpin loop features

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

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

Internal loop features
Number of internal loops [?]:1
Maximum number of free bases in internal loops:3
Average number of free bases in internal loops:2.5
Minimum number of free bases in internal loop:2
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:1
Minimum internal loop absolute asymmetry:1
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 [?]: 2
Total number of AG non-canonical base pairs:2

Pseudoknot features



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