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

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General features for molecule PDB_00715
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00715
Molecule name [?]:CRYSTAL STRUCTURE OF A C75U MUTANT HEPATITIS DELTA VIRUS RIBOZYME PRECURSOR, IN CU2+ SOLUTION
Source [?]:RCSB Protein Data Bank
Source ID [?]:1SJ4
Reference [?]:A.KE,K.ZHOU,F.DING,J.H.CATE,J.A.DOUDNA. A CONFORMATIONAL SWITCH CONTROLS HEPATITIS DELTA VIRUS RIBOZYME CATALYSIS. NATURE V. 429 201 2004 ASTM NATUAS UK ISSN 0028-0836
Type [?]:Other Ribozyme

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:HEPATITIS DELTA VIRUS
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 2.70 ANGSTROMS; ran through RNAview
Number of molecules [?]:1
Length [?]:73
Fragments used [?]:Yes
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00714, PDB_00760, PDB_00761, PDB_00762, PDB_00763, PDB_01185, PDB_01190
Number of domains [?]:1
Number of unpaired bases [?]:27
Number of paired bases [?]:46

Click on any header below for additional features.

Stem features

Number of stems [?]:1
Number of base pairs in stems [?]:5
Maximum length of a stem [?]:5
Average length of a stem [?]:5
Minimum length of a stem [?]:5
Maximum estimated free energy [?]:-7.6
Average estimated free energy [?]:-7.6
Minimum estimated free energy [?]:-7.6

Hairpin loop features

Number of hairpin loops [?]:1
Maximum number of free bases in hairpin loops [?]:10
Average number of free bases in hairpin loops [?]:10
Minimum number of free bases in hairpin loop [?]:10

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

Multi-loop features

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

Pseudoknot features
Number of pseudoknots [?]:1
Number of bands:4
Number of base pairs in bands:18
Maximum band length:7
Average band length:4.5
Minimum band length:2
Maximum number of bands per pseudoknot:4
Average number of bands per pseudoknot:4
Minimum number of bands per pseudoknot:4
Maximum number of un-bands:1
Average number of un-bands:1
Minimum number of un-bands:1
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:16
Average number of unpaired bases:16
Minimum number of unpaired bases:16
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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