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

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General features for molecule PDB_00651
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00651
Molecule name [?]:CRYSTAL STRUCTURE OF CCDAP-PUROMYCIN BOUND AT THE PEPTIDYL TRANSFERASE CENTER OF THE 50S RIBOSOMAL S
Source [?]:RCSB Protein Data Bank
Source ID [?]:1Q7Y
Reference [?]:J.L.HANSEN,T.M.SCHMEING,P.B.MOORE,T.A.STEITZ. STRUCTURAL INSIGHTS INTO PEPTIDE BOND FORMATION. PROC.NATL.ACAD.SCI.USA V. 99 11670 2002 ASTM PNASA6 US ISSN 0027-8424
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 3.20 ANGSTROMS; ran through RNAview
Number of molecules [?]:3
Length [?]:2880
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:944
Number of paired bases [?]:1936

Click on any header below for additional features.

Stem features

Number of stems [?]:140
Number of base pairs in stems [?]:729
Maximum length of a stem [?]:13
Average length of a stem [?]:5.21
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-7.58
Minimum estimated free energy [?]:-25.2

Hairpin loop features

Number of hairpin loops [?]:57
Maximum number of free bases in hairpin loops [?]:9
Average number of free bases in hairpin loops [?]:4.23
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 [?]:26
Maximum number of free bases in internal loops:6
Average number of free bases in internal loops:2.4
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:4
Average internal loop absolute asymmetry:1.19
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.69
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 [?]: 132
Total number of AA non-canonical base pairs:16
Total number of AC non-canonical base pairs:16
Total number of AG non-canonical base pairs:68
Total number of CC non-canonical base pairs:12
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:25
Number of base pairs in bands:239
Maximum band length:38
Average band length:9.56
Minimum band length:2
Maximum number of bands per pseudoknot:12
Average number of bands per pseudoknot:4.17
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:12
Average number of un-bands:2.17
Minimum number of un-bands:0
Maximum number of in-bands:20
Average number of in-bands:3.83
Minimum number of in-bands:0
Maximum number of unpaired bases:243
Average number of unpaired bases:55.5
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:29
Maximum number of base pairs to remove, per pseudoknot:12
Average number of base pairs to remove, per pseudoknot:4.83
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:10
Maximum number of bands to remove, per pseudoknot:4
Average number of bands to remove, per pseudoknot:1.67
Minimum number of bands to remove, per pseudoknot:1



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