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

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General features for molecule PDB_01068
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_01068
Molecule name [?]:PRE-CLEAVAGE STATE OF THE THERMOANAEROBACTER TENGCONGENSIS GLMS RIBOZYME
Source [?]:RCSB Protein Data Bank
Source ID [?]:2GCS
Reference [?]:D.J.KLEIN,A.R.FERRE-D'AMARE. STRUCTURAL BASIS OF GLMS RIBOZYME ACTIVATION BY GLUCOSAMINE-6-PHOSPHATE. SCIENCE V. 313 1752 2006 ASTM SCIEAS US ISSN 0036-8075
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 2.10 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:142
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_01094, PDB_01095, PDB_01110
Number of domains [?]:2
Number of unpaired bases [?]:36
Number of paired bases [?]:106

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:28
Maximum length of a stem [?]:11
Average length of a stem [?]:9.33
Minimum length of a stem [?]:7
Maximum estimated free energy [?]:-11.8
Average estimated free energy [?]:-14.1
Minimum estimated free energy [?]:-18.4

Hairpin loop features

Number of hairpin loops [?]:2
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 [?]: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:4
Average number of free bases in internal loops:3
Minimum number of free bases in internal loop:2
Maximum internal loop absolute asymmetry:2
Average internal loop absolute asymmetry:2
Minimum internal loop absolute asymmetry:2
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 [?]: 4
Total number of AA non-canonical base pairs:1
Total number of AC non-canonical base pairs:1
Total number of AG non-canonical base pairs:2

Pseudoknot features
Number of pseudoknots [?]:2
Number of bands:4
Number of base pairs in bands:25
Maximum band length:8
Average band length:6.25
Minimum band length:5
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:1
Average number of un-bands:0.5
Minimum number of un-bands:0
Maximum number of in-bands:1
Average number of in-bands:0.5
Minimum number of in-bands:0
Maximum number of unpaired bases:17
Average number of unpaired bases:11.5
Minimum number of unpaired bases:6
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:11
Maximum number of base pairs to remove, per pseudoknot:6
Average number of base pairs to remove, per pseudoknot:5.5
Minimum number of base pairs to remove, per pseudoknot:5
Minimum number of bands to remove, per molecule:2
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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