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

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General features for molecule PDB_00827
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00827
Molecule name [?]:CRYSTAL STRUCTURE OF AN ACTIVE GROUP I RIBOZYME-PRODUCT COMPLEX
Source [?]:RCSB Protein Data Bank
Source ID [?]:1Y0Q
Reference [?]:B.L.GOLDEN,H.KIM,E.CHASE. CRYSTAL STRUCTURE OF A PHAGE TWORT GROUP I RIBOZYME-PRODUCT COMPLEX. NAT.STRUCT.MOL.BIOL. V. 12 82 2005 US ISSN 1545-9993
Type [?]:Other Ribozyme

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:BACTERIOPHAGE TWORT
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 3.60 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:233
Fragments used [?]:Yes
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:71
Number of paired bases [?]:162

Click on any header below for additional features.

Stem features

Number of stems [?]:10
Number of base pairs in stems [?]:52
Maximum length of a stem [?]:10
Average length of a stem [?]:5.2
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:-1.3
Average estimated free energy [?]:-6.31
Minimum estimated free energy [?]:-11.4

Hairpin loop features

Number of hairpin loops [?]:6
Maximum number of free bases in hairpin loops [?]:5
Average number of free bases in hairpin loops [?]:2.33
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 [?]:3
Maximum number of free bases in internal loops:2
Average number of free bases in internal loops:1.33
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:0.67
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:1.67
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:1
Maximum number of free bases in multi-loops:4
Average number of free bases in multi-loops:1.67
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:4
Average multi-loop absolute asymmetry:2.67
Minimum multi-loop absolute asymmetry:1
Maximum multi-loop relative asymmetry:4
Average multi-loop relative asymmetry:1.06
Minimum multi-loop relative asymmetry:0
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 [?]: 9
Total number of AA non-canonical base pairs:2
Total number of AG non-canonical base pairs:5
Total number of CU non-canonical base pairs:1
Total number of UU non-canonical base pairs:1

Pseudoknot features
Number of pseudoknots [?]:1
Number of bands:5
Number of base pairs in bands:29
Maximum band length:10
Average band length:5.8
Minimum band length:3
Maximum number of bands per pseudoknot:5
Average number of bands per pseudoknot:5
Minimum number of bands per pseudoknot:5
Maximum number of un-bands:4
Average number of un-bands:4
Minimum number of un-bands:4
Maximum number of in-bands:1
Average number of in-bands:1
Minimum number of in-bands:1
Maximum number of unpaired bases:44
Average number of unpaired bases:44
Minimum number of unpaired bases:44
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:8
Maximum number of base pairs to remove, per pseudoknot:8
Average number of base pairs to remove, per pseudoknot:8
Minimum number of base pairs to remove, per pseudoknot:8
Minimum number of bands to remove, per molecule:2
Maximum number of bands to remove, per pseudoknot:2
Average number of bands to remove, per pseudoknot:2
Minimum number of bands to remove, per pseudoknot:2



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