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

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General features for molecule PDB_01221
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_01221
Molecule name [?]:CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH NEOMYCIN. THIS FIL
Source [?]:RCSB Protein Data Bank
Source ID [?]:2QAM
Reference [?]:M.A.BOROVINSKAYA,R.D.PAI,W.ZHANG,B.S.SCHUWIRTH, J.M.HOLTON,G.HIROKAWA,H.KAJI,A.KAJI,J.H.CATE. STRUCTURAL BASIS FOR AMINOGLYCOSIDE INHIBITION OF BACTERIAL RIBOSOME RECYCLING.. NAT.STRUCT.MOL.BIOL. V. 14 727 2007 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, RESOLUTION 3.21 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:2958
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00792, PDB_00794, PDB_00934, PDB_00936, PDB_01121, PDB_01123, PDB_01223, PDB_01225, PDB_01227, PDB_01229, PDB_01231, PDB_01233, PDB_01235, PDB_01242, PDB_01244, PDB_01246, PDB_01248, PDB_01283, PDB_01285
Number of domains [?]:2
Number of unpaired bases [?]:960
Number of paired bases [?]:1998

Click on any header below for additional features.

Stem features

Number of stems [?]:144
Number of base pairs in stems [?]:762
Maximum length of a stem [?]:17
Average length of a stem [?]:5.3
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-7.43
Minimum estimated free energy [?]:-21.1

Hairpin loop features

Number of hairpin loops [?]:58
Maximum number of free bases in hairpin loops [?]:9
Average number of free bases in hairpin loops [?]:4.62
Minimum number of free bases in hairpin loop [?]:1
Total number of UUCG hairpin motifs per molecule [?]:1

Bulge loop features
Number of bulge loops [?]:42
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 [?]:27
Maximum number of free bases in internal loops:5
Average number of free bases in internal loops:1.96
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:0.74
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.52
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:16
Maximum number of free bases in multi-loops:20
Average number of free bases in multi-loops:3.12
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:20
Average multi-loop absolute asymmetry:3.21
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:20
Average multi-loop relative asymmetry:1.29
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:5
Average number of branches in multi-loops:3.75
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 121
Total number of AA non-canonical base pairs:20
Total number of AC non-canonical base pairs:5
Total number of AG non-canonical base pairs:76
Total number of CC non-canonical base pairs:2
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:9

Pseudoknot features
Number of pseudoknots [?]:6
Number of bands:22
Number of base pairs in bands:237
Maximum band length:40
Average band length:10.77
Minimum band length:2
Maximum number of bands per pseudoknot:9
Average number of bands per pseudoknot:3.67
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:7
Average number of un-bands:1.33
Minimum number of un-bands:0
Maximum number of in-bands:23
Average number of in-bands:4.33
Minimum number of in-bands:0
Maximum number of unpaired bases:252
Average number of unpaired bases:55.83
Minimum number of unpaired bases:8
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:25
Maximum number of base pairs to remove, per pseudoknot:10
Average number of base pairs to remove, per pseudoknot:4.17
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:9
Maximum number of bands to remove, per pseudoknot:3
Average number of bands to remove, per pseudoknot:1.5
Minimum number of bands to remove, per pseudoknot:1



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