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

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General features for molecule PDB_00404
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00404
Molecule name [?]:LARGE RIBOSOMAL SUBUNIT COMPLEXED WITH A 13 BP MINIHELIX- PUROMYCIN COMPOUND
Source [?]:RCSB Protein Data Bank
Source ID [?]:1FG0
Reference [?]:P.NISSEN,J.HANSEN,N.BAN,P.B.MOORE,T.A.STEITZ. THE STRUCTURAL BASIS OF RIBOSOME ACTIVITY IN PEPTIDE BOND SYNTHESIS.. SCIENCE V. 289 920 2000 ASTM SCIEAS US ISSN 0036-8075
Type [?]:Other Ribosomal RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:HALOARCULA MARISMORTUI
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 3.00 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:499
Fragments used [?]:Yes
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:2
Number of unpaired bases [?]:195
Number of paired bases [?]:304

Click on any header below for additional features.

Stem features

Number of stems [?]:32
Number of base pairs in stems [?]:138
Maximum length of a stem [?]:11
Average length of a stem [?]:4.31
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-6.67
Minimum estimated free energy [?]:-16.3

Hairpin loop features

Number of hairpin loops [?]:12
Maximum number of free bases in hairpin loops [?]:8
Average number of free bases in hairpin loops [?]:4.17
Minimum number of free bases in hairpin loop [?]:2

Bulge loop features
Number of bulge loops [?]:12
Maximum number of free bases in bulge loops [?]:2
Average number of free bases in bulge loops [?]:0.71
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:4
Maximum number of free bases in internal loops:3
Average number of free bases in internal loops:2.12
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:0.75
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:1.25
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:4
Maximum number of free bases in multi-loops:16
Average number of free bases in multi-loops:5.06
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:14
Average multi-loop absolute asymmetry:3.3
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:8
Average multi-loop relative asymmetry:1.3
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:5
Average number of branches in multi-loops:4
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 17
Total number of AA non-canonical base pairs:2
Total number of AC non-canonical base pairs:1
Total number of AG non-canonical base pairs:9
Total number of CC non-canonical base pairs:2
Total number of CU non-canonical base pairs:1
Total number of UU non-canonical base pairs:2

Pseudoknot features
Number of pseudoknots [?]:1
Number of bands:2
Number of base pairs in bands:14
Maximum band length:11
Average band length:7
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:3
Average number of in-bands:3
Minimum number of in-bands:3
Maximum number of unpaired bases:21
Average number of unpaired bases:21
Minimum number of unpaired bases:21
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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