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

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General features for molecule PDB_00604
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00604
Molecule name [?]:STRUCTURE OF CHLORAMPHENICOL BOUND TO THE 50S RIBOSOMAL SUBUNIT
Source [?]:RCSB Protein Data Bank
Source ID [?]:1NJI
Reference [?]:J.HANSEN,P.B.MOORE,T.A.STEITZ. STRUCTURES OF FIVE ANTIBIOTICS BOUND AT THE PEPTIDYL TRANSFERASE CENTER OF THE LARGE RIBOSOMAL SUBUNIT. J.MOL.BIOL. V. 330 1061 2003 ASTM JMOBAK UK ISSN 0022-2836
Type [?]:23S 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 [?]:2876
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00488, PDB_00510, PDB_00511, PDB_00514, PDB_00518, PDB_00554, PDB_00595, PDB_00797
Number of domains [?]:3
Number of unpaired bases [?]:942
Number of paired bases [?]:1934

Click on any header below for additional features.

Stem features

Number of stems [?]:143
Number of base pairs in stems [?]:732
Maximum length of a stem [?]:13
Average length of a stem [?]:5.12
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-7.43
Minimum estimated free energy [?]:-25.2

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 [?]:4.24
Minimum number of free bases in hairpin loop [?]:1

Bulge loop features
Number of bulge loops [?]:42
Maximum number of free bases in bulge loops [?]:4
Average number of free bases in bulge loops [?]:0.76
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:28
Maximum number of free bases in internal loops:6
Average number of free bases in internal loops:2.27
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:1.11
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.71
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:15
Maximum number of free bases in multi-loops:20
Average number of free bases in multi-loops:3.16
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:20
Average multi-loop absolute asymmetry:3.13
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:20
Average multi-loop relative asymmetry:1.24
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:5
Average number of branches in multi-loops:3.73
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 136
Total number of AA non-canonical base pairs:18
Total number of AC non-canonical base pairs:17
Total number of AG non-canonical base pairs:68
Total number of CC non-canonical base pairs:13
Total number of CU non-canonical base pairs:9
Total number of GG non-canonical base pairs:1
Total number of UU non-canonical base pairs:10

Pseudoknot features
Number of pseudoknots [?]:6
Number of bands:22
Number of base pairs in bands:235
Maximum band length:38
Average band length:10.68
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:24
Average number of in-bands:4.5
Minimum number of in-bands:0
Maximum number of unpaired bases:231
Average number of unpaired bases:52.83
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:27
Maximum number of base pairs to remove, per pseudoknot:10
Average number of base pairs to remove, per pseudoknot:4.5
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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