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

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General features for molecule PDB_00005
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00005
Molecule name [?]:NMR STRUCTURE OF A CLASSICAL PSEUDOKNOT: INTERPLAY OF SINGLE-AND DOUBLE-STRANDED RNA, 24 STRUCTURES
Source [?]:RCSB Protein Data Bank
Source ID [?]:1A60
Reference [?]:M.H.KOLK,M.VAN DER GRAAF,S.S.WIJMENGA,C.W.PLEIJ, H.A.HEUS,C.W.HILBERS. NMR STRUCTURE OF A CLASSICAL PSEUDOKNOT: INTERPLAY OF SINGLE- AND DOUBLE-STRANDED RNA.. SCIENCE V. 280 434 1998 ASTM SCIEAS US ISSN 0036-8075
Type [?]:Other RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:N/A
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:NMR; ran through RNAview
Number of molecules [?]:1
Length [?]:44
Fragments used [?]:Yes
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:2
Number of unpaired bases [?]:16
Number of paired bases [?]:28

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 [?]:-11.1
Average estimated free energy [?]:-11.1
Minimum estimated free energy [?]:-11.1

Hairpin loop features

Number of hairpin loops [?]:1
Maximum number of free bases in hairpin loops [?]:7
Average number of free bases in hairpin loops [?]:7
Minimum number of free bases in hairpin loop [?]:7

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 [?]: 0

Pseudoknot features
Number of pseudoknots [?]:1
Number of bands:2
Number of base pairs in bands:9
Maximum band length:6
Average band length:4.5
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:0
Average number of un-bands:0
Minimum number of un-bands:0
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:6
Average number of unpaired bases:6
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:3
Maximum number of base pairs to remove, per pseudoknot:3
Average number of base pairs to remove, per pseudoknot:3
Minimum number of base pairs to remove, per pseudoknot:3
Minimum number of bands to remove, per molecule:1
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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