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

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General features for molecule PDB_00880
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00880
Molecule name [?]:CRYSTAL STRUCTURE OF A COMPLEX OF THE RIBOSOME LARGE SUBUNIT WITH RAPAMYCIN
Source [?]:RCSB Protein Data Bank
Source ID [?]:1Z58
Reference [?]:M.AMIT,R.BERISIO,D.BARAM,J.HARMS,A.BASHAN,A.YONATH. A CREVICE ADJOINING THE RIBOSOME TUNNEL: HINTS FOR COTRANSLATIONAL FOLDING.. FEBS LETT. V. 579 3207 2005 ASTM FEBLAL NE ISSN 0014-5793
Type [?]:23S Ribosomal RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:DEINOCOCCUS RADIODURANS
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 3.80 ANGSTROMS; ran through RNAview
Number of molecules [?]:1
Length [?]:2766
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00606, PDB_00922, PDB_01173, PDB_01174, PDB_01175, PDB_01182, PDB_01183
Number of domains [?]:1
Number of unpaired bases [?]:1566
Number of paired bases [?]:1200

Click on any header below for additional features.

Stem features

Number of stems [?]:154
Number of base pairs in stems [?]:515
Maximum length of a stem [?]:10
Average length of a stem [?]:3.34
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0.3
Average estimated free energy [?]:-4.6
Minimum estimated free energy [?]:-19.5

Hairpin loop features

Number of hairpin loops [?]:57
Maximum number of free bases in hairpin loops [?]:72
Average number of free bases in hairpin loops [?]:8.98
Minimum number of free bases in hairpin loop [?]:2
Total number of UUCG hairpin motifs per molecule [?]:1

Bulge loop features
Number of bulge loops [?]:18
Maximum number of free bases in bulge loops [?]:3
Average number of free bases in bulge loops [?]:0.89
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:59
Maximum number of free bases in internal loops:23
Average number of free bases in internal loops:2.95
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:15
Average internal loop absolute asymmetry:1.08
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.29
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:20
Maximum number of free bases in multi-loops:22
Average number of free bases in multi-loops:4.66
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:20
Average multi-loop absolute asymmetry:3.59
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:11
Average multi-loop relative asymmetry:1.37
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
Average number of branches in multi-loops:3.85
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 71
Total number of AA non-canonical base pairs:6
Total number of AC non-canonical base pairs:9
Total number of AG non-canonical base pairs:40
Total number of CC non-canonical base pairs:3
Total number of CU non-canonical base pairs:6
Total number of GG non-canonical base pairs:3
Total number of UU non-canonical base pairs:4

Pseudoknot features
Number of pseudoknots [?]:4
Number of bands:10
Number of base pairs in bands:85
Maximum band length:26
Average band length:8.5
Minimum band length:2
Maximum number of bands per pseudoknot:3
Average number of bands per pseudoknot:2.5
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:5
Average number of un-bands:2.25
Minimum number of un-bands:0
Maximum number of in-bands:14
Average number of in-bands:3.5
Minimum number of in-bands:0
Maximum number of unpaired bases:234
Average number of unpaired bases:78.5
Minimum number of unpaired bases:25
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:14
Maximum number of base pairs to remove, per pseudoknot:5
Average number of base pairs to remove, per pseudoknot:3.5
Minimum number of base pairs to remove, per pseudoknot:3
Minimum number of bands to remove, per molecule:4
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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