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

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



General features for molecule PDB_00502
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00502
Molecule name [?]:STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTER
Source [?]:RCSB Protein Data Bank
Source ID [?]:1JZZ
Reference [?]:F.SCHLUNZEN,R.ZARIVACH,J.HARMS,A.BASHAN,A.TOCILJ, R.ALBRECHT,A.YONATH,F.FRANCESCHI. STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTRE IN EUBACTERIA.. NATURE V. 413 814 2001 ASTM NATUAS UK ISSN 0028-0836
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 3.80 ANGSTROMS; ran through RNAview
Number of molecules [?]:1
Length [?]:2774
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00477, PDB_00500, PDB_00501, PDB_00503
Number of domains [?]:1
Number of unpaired bases [?]:1260
Number of paired bases [?]:1514

Click on any header below for additional features.

Stem features

Number of stems [?]:143
Number of base pairs in stems [?]:559
Maximum length of a stem [?]:11
Average length of a stem [?]:3.91
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-5.66
Minimum estimated free energy [?]:-19.5

Hairpin loop features

Number of hairpin loops [?]:58
Maximum number of free bases in hairpin loops [?]:13
Average number of free bases in hairpin loops [?]:5.84
Minimum number of free bases in hairpin loop [?]:2

Bulge loop features
Number of bulge loops [?]:25
Maximum number of free bases in bulge loops [?]:3
Average number of free bases in bulge loops [?]:0.68
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:45
Maximum number of free bases in internal loops:14
Average number of free bases in internal loops:2.94
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:6
Average internal loop absolute asymmetry:0.91
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.22
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:15
Maximum number of free bases in multi-loops:14
Average number of free bases in multi-loops:3.78
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:14
Average multi-loop absolute asymmetry:2.94
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:10
Average multi-loop relative asymmetry:1.36
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 [?]: 80
Total number of AA non-canonical base pairs:7
Total number of AC non-canonical base pairs:12
Total number of AG non-canonical base pairs:42
Total number of CC non-canonical base pairs:3
Total number of CU non-canonical base pairs:6
Total number of GG non-canonical base pairs:5
Total number of UU non-canonical base pairs:5

Pseudoknot features
Number of pseudoknots [?]:5
Number of bands:18
Number of base pairs in bands:198
Maximum band length:33
Average band length:11
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:7
Average number of un-bands:1.6
Minimum number of un-bands:0
Maximum number of in-bands:23
Average number of in-bands:5.2
Minimum number of in-bands:0
Maximum number of unpaired bases:321
Average number of unpaired bases:80.4
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



    [ 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