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

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General features for molecule PDB_00805
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00805
Molecule name [?]:STRUCTURE OF THE TETRAHYMENA RIBOZYME: BASE TRIPLE SANDWICH AND METAL ION AT THE ACTIVE SITE
Source [?]:RCSB Protein Data Bank
Source ID [?]:1X8W
Reference [?]:F.GUO,A.R.GOODING,T.R.CECH. STRUCTURE OF THE TETRAHYMENA RIBOZYME: BASE TRIPLE SANDWICH AND METAL ION AT THE ACTIVE SITE.. MOL.CELL V. 16 351 2004 ASTM MOCEFL US ISSN 1097-2765
Type [?]:Other Ribozyme

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:TETRAHYMENA THERMOPHILA
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 3.80 ANGSTROMS; ran through RNAview
Number of molecules [?]:4
Length [?]:968
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:8
Number of unpaired bases [?]:364
Number of paired bases [?]:604

Click on any header below for additional features.

Stem features

Number of stems [?]:56
Number of base pairs in stems [?]:264
Maximum length of a stem [?]:10
Average length of a stem [?]:4.71
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:-2.5
Average estimated free energy [?]:-7.12
Minimum estimated free energy [?]:-13.6

Hairpin loop features

Number of hairpin loops [?]:20
Maximum number of free bases in hairpin loops [?]:7
Average number of free bases in hairpin loops [?]:3.75
Minimum number of free bases in hairpin loop [?]:2

Bulge loop features
Number of bulge loops [?]:13
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 [?]:19
Maximum number of free bases in internal loops:6
Average number of free bases in internal loops:2.97
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:5
Average internal loop absolute asymmetry:1.63
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:6
Average internal loop relative asymmetry:2.11
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:4
Maximum number of free bases in multi-loops:4
Average number of free bases in multi-loops:2.5
Minimum number of free bases in multi-loop:1
Maximum multi-loop absolute asymmetry:3
Average multi-loop absolute asymmetry:1.5
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:4
Average multi-loop relative asymmetry:1.42
Minimum multi-loop relative asymmetry:0.25
Maximum number of branches in multi-loops:3
Average number of branches in multi-loops:3
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 24
Total number of AA non-canonical base pairs:4
Total number of AG non-canonical base pairs:16
Total number of UU non-canonical base pairs:4

Pseudoknot features
Number of pseudoknots [?]:4
Number of bands:8
Number of base pairs in bands:38
Maximum band length:6
Average band length:4.75
Minimum band length:3
Maximum number of bands per pseudoknot:2
Average number of bands per pseudoknot:2
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:3
Average number of un-bands:3
Minimum number of un-bands:3
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:27
Average number of unpaired bases:22.75
Minimum number of unpaired bases:20
Several ways to remove minimum number of base pairs, per molecule:Yes
Minimum number of base pairs to remove, per molecule:17
Maximum number of base pairs to remove, per pseudoknot:5
Average number of base pairs to remove, per pseudoknot:4.25
Minimum number of base pairs to remove, per pseudoknot:3
Minimum number of bands to remove, per molecule:4
Maximum number of bands to remove, per pseudoknot:1
Average number of bands to remove, per pseudoknot:1
Minimum number of bands to remove, per pseudoknot:1



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