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

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General features for molecule PDB_00776
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00776
Molecule name [?]:CRYSTAL STRUCTURE OF FIVE 70S RIBOSOMES FROM ESCHERICHIA COLI IN COMPLEX WITH PROTEIN Y. THIS FILE C
Source [?]:RCSB Protein Data Bank
Source ID [?]:1VOY
Reference [?]:A.VILA-SANJURJO,B.S.SCHUWIRTH,C.W.HAU,J.H.CATE. STRUCTURAL BASIS FOR THE CONTROL OF TRANSLATION INITIATION DURING STRESS.. NAT.STRUCT.MOL.BIOL. V. 11 1054 2004 US ISSN 1545-9993
Type [?]:23S Ribosomal RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:ESCHERICHIA COLI
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION11.50 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:2943
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00770, PDB_00772, PDB_00774, PDB_00778
Number of domains [?]:2
Number of unpaired bases [?]:1683
Number of paired bases [?]:1260

Click on any header below for additional features.

Stem features

Number of stems [?]:151
Number of base pairs in stems [?]:550
Maximum length of a stem [?]:10
Average length of a stem [?]:3.64
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-5.61
Minimum estimated free energy [?]:-16

Hairpin loop features

Number of hairpin loops [?]:56
Maximum number of free bases in hairpin loops [?]:22
Average number of free bases in hairpin loops [?]:7.52
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 [?]:10
Maximum number of free bases in bulge loops [?]:3
Average number of free bases in bulge loops [?]:0.75
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:65
Maximum number of free bases in internal loops:84
Average number of free bases in internal loops:4.95
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:80
Average internal loop absolute asymmetry:3.4
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:22
Average internal loop relative asymmetry:2.25
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:20
Maximum number of free bases in multi-loops:23
Average number of free bases in multi-loops:4.61
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:21
Average multi-loop absolute asymmetry:4.38
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:13
Average multi-loop relative asymmetry:1.63
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
Average number of branches in multi-loops:3.7
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 46
Total number of AA non-canonical base pairs:3
Total number of AC non-canonical base pairs:2
Total number of AG non-canonical base pairs:31
Total number of CC non-canonical base pairs:1
Total number of CU non-canonical base pairs:2
Total number of GG non-canonical base pairs:2
Total number of UU non-canonical base pairs:5

Pseudoknot features
Number of pseudoknots [?]:3
Number of bands:7
Number of base pairs in bands:80
Maximum band length:31
Average band length:11.43
Minimum band length:2
Maximum number of bands per pseudoknot:3
Average number of bands per pseudoknot:2.33
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:5
Average number of un-bands:1.67
Minimum number of un-bands:0
Maximum number of in-bands:15
Average number of in-bands:6
Minimum number of in-bands:0
Maximum number of unpaired bases:212
Average number of unpaired bases:82
Minimum number of unpaired bases:11
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:4
Average number of base pairs to remove, per pseudoknot:2.67
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:3
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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