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

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General features for molecule PDB_00078
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00078
Molecule name [?]:CRYSTAL STRUCTURE OF A GROUP I RIBOZYME DOMAIN: PRINCIPLES OF RNA PACKING
Source [?]:RCSB Protein Data Bank
Source ID [?]:1GID
Reference [?]:J.H.CATE,A.R.GOODING,E.PODELL,K.ZHOU,B.L.GOLDEN, C.E.KUNDROT,T.R.CECH,J.A.DOUDNA. CRYSTAL STRUCTURE OF A GROUP I RIBOZYME DOMAIN: PRINCIPLES OF RNA PACKING.. SCIENCE V. 273 1678 1996 ASTM SCIEAS US ISSN 0036-8075
Type [?]:Other Ribozyme

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:N/A
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 2.50 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:316
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:86
Number of paired bases [?]:230

Click on any header below for additional features.

Stem features

Number of stems [?]:6
Number of base pairs in stems [?]:48
Maximum length of a stem [?]:11
Average length of a stem [?]:8
Minimum length of a stem [?]:4
Maximum estimated free energy [?]:-7.1
Average estimated free energy [?]:-12.1
Minimum estimated free energy [?]:-15.6

Hairpin loop features

Number of hairpin loops [?]:4
Maximum number of free bases in hairpin loops [?]:4
Average number of free bases in hairpin loops [?]:3.5
Minimum number of free bases in hairpin loop [?]:3

Bulge loop features
Number of bulge loops [?]:0
Maximum number of free bases in bulge loops [?]:N/A
Average number of free bases in bulge loops [?]:N/A
Minimum number of free bases in bulge loop [?]:N/A

Internal loop features
Number of internal loops [?]:2
Maximum number of free bases in internal loops:3
Average number of free bases in internal loops:2.5
Minimum number of free bases in internal loop:2
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:1
Minimum internal loop absolute asymmetry:1
Maximum internal loop relative asymmetry:1
Average internal loop relative asymmetry:1
Minimum internal loop relative asymmetry:1

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 4
Total number of AG non-canonical base pairs:4

Pseudoknot features
Number of pseudoknots [?]:2
Number of bands:4
Number of base pairs in bands:67
Maximum band length:32
Average band length:16.75
Minimum band length:2
Maximum number of bands per pseudoknot:2
Average number of bands per pseudoknot:2
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:3
Average number of un-bands:1.5
Minimum number of un-bands:0
Maximum number of in-bands:1
Average number of in-bands:1
Minimum number of in-bands:1
Maximum number of unpaired bases:29
Average number of unpaired bases:28.5
Minimum number of unpaired bases:28
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:4
Maximum number of base pairs to remove, per pseudoknot:2
Average number of base pairs to remove, per pseudoknot:2
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:2
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



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