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

    [ Home | Search | Analyse | Submit structures | News | Help ]



General features for molecule PDB_00808
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00808
Molecule name [?]:INHIBITION OF PEPTIDE BOND FORMATION BY PLEUROMUTILINS: THE STRUCTURE OF THE 50S RIBOSOMAL SUBUNIT F
Source [?]:RCSB Protein Data Bank
Source ID [?]:1XBP
Reference [?]:F.SCHLUENZEN,E.PYETAN,P.FUCINI,A.YONATH,J.M.HARMS. INHIBITION OF PEPTIDE BOND FORMATION BY PLEUROMUTILINS: THE STRUCTURE OF THE 50S RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS IN COMPLEX WITH TIAMULIN.. MOL.MICROBIOL. V. 54 1287 2004 ASTM MOMIEE UK ISSN 0950-382X
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_00615, PDB_00616, PDB_00719, PDB_00833
Number of domains [?]:2
Number of unpaired bases [?]:1428
Number of paired bases [?]:1456

Click on any header below for additional features.

Stem features

Number of stems [?]:168
Number of base pairs in stems [?]:632
Maximum length of a stem [?]:10
Average length of a stem [?]:3.76
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-5.82
Minimum estimated free energy [?]:-20

Hairpin loop features

Number of hairpin loops [?]:61
Maximum number of free bases in hairpin loops [?]:17
Average number of free bases in hairpin loops [?]:6.34
Minimum number of free bases in hairpin loop [?]:0

Bulge loop features
Number of bulge loops [?]:17
Maximum number of free bases in bulge loops [?]:3
Average number of free bases in bulge loops [?]:0.82
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:67
Maximum number of free bases in internal loops:18
Average number of free bases in internal loops:2.9
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:16
Average internal loop absolute asymmetry:1.15
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:9
Average internal loop relative asymmetry:1.52
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:23
Maximum number of free bases in multi-loops:25
Average number of free bases in multi-loops:3.99
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:21
Average multi-loop absolute asymmetry:2.98
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:22
Average multi-loop relative asymmetry:1.34
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
Average number of branches in multi-loops:3.78
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 58
Total number of AA non-canonical base pairs:5
Total number of AC non-canonical base pairs:3
Total number of AG non-canonical base pairs:36
Total number of CC non-canonical base pairs:1
Total number of CU non-canonical base pairs:4
Total number of GG non-canonical base pairs:4
Total number of UU non-canonical base pairs:5

Pseudoknot features
Number of pseudoknots [?]:5
Number of bands:12
Number of base pairs in bands:96
Maximum band length:30
Average band length:8
Minimum band length:2
Maximum number of bands per pseudoknot:3
Average number of bands per pseudoknot:2.4
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:5
Average number of un-bands:1.8
Minimum number of un-bands:0
Maximum number of in-bands:14
Average number of in-bands:2.8
Minimum number of in-bands:0
Maximum number of unpaired bases:202
Average number of unpaired bases:55.2
Minimum number of unpaired bases:5
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:16
Maximum number of base pairs to remove, per pseudoknot:5
Average number of base pairs to remove, per pseudoknot:3.2
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:5
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



    [ Home | Search | Analyse | Submit structures | News | Help ]

For questions, comments, suggestions and bug reports, please contact:

Copyright © 2004-2008 BETA LAB - University of British Columbia