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

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General features for molecule PDB_00615
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00615
Molecule name [?]:COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773
Source [?]:RCSB Protein Data Bank
Source ID [?]:1NWX
Reference [?]:F.SCHLUNZEN,J.M.HARMS,F.FRANCESCHI,H.A.HANSEN, H.BARTELS,R.ZARIVACH,A.YONATH. STRUCTURAL BASIS FOR THE ANTIBIOTIC ACTIVITY OF KETOLIDES AND AZALIDES.. STRUCTURE V. 11 329 2003 ASTM STRUE6 UK ISSN 0969-2126
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 3.50 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:2884
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00609, PDB_00616, PDB_00719, PDB_00808, PDB_00833
Number of domains [?]:2
Number of unpaired bases [?]:1324
Number of paired bases [?]:1560

Click on any header below for additional features.

Stem features

Number of stems [?]:146
Number of base pairs in stems [?]:591
Maximum length of a stem [?]:12
Average length of a stem [?]:4.05
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-6.47
Minimum estimated free energy [?]:-20

Hairpin loop features

Number of hairpin loops [?]:58
Maximum number of free bases in hairpin loops [?]:15
Average number of free bases in hairpin loops [?]:5.9
Minimum number of free bases in hairpin loop [?]:0

Bulge loop features
Number of bulge loops [?]:21
Maximum number of free bases in bulge loops [?]:3
Average number of free bases in bulge loops [?]:0.74
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:52
Maximum number of free bases in internal loops:20
Average number of free bases in internal loops:2.97
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:15
Average internal loop absolute asymmetry:1.21
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.48
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:15
Maximum number of free bases in multi-loops:15
Average number of free bases in multi-loops:3.74
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:15
Average multi-loop absolute asymmetry:3.1
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:10
Average multi-loop relative asymmetry:1.3
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
Average number of branches in multi-loops:3.87
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 51
Total number of AA non-canonical base pairs:5
Total number of AC non-canonical base pairs:6
Total number of AG non-canonical base pairs:33
Total number of CU non-canonical base pairs:5
Total number of GG non-canonical base pairs:1
Total number of UU non-canonical base pairs:1

Pseudoknot features
Number of pseudoknots [?]:5
Number of bands:18
Number of base pairs in bands:189
Maximum band length:33
Average band length:10.5
Minimum band length:2
Maximum number of bands per pseudoknot:9
Average number of bands per pseudoknot:3.6
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:8
Average number of un-bands:2
Minimum number of un-bands:0
Maximum number of in-bands:21
Average number of in-bands:4.6
Minimum number of in-bands:0
Maximum number of unpaired bases:323
Average number of unpaired bases:84.4
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:22
Maximum number of base pairs to remove, per pseudoknot:10
Average number of base pairs to remove, per pseudoknot:4.4
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:7
Maximum number of bands to remove, per pseudoknot:3
Average number of bands to remove, per pseudoknot:1.4
Minimum number of bands to remove, per pseudoknot:1



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