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

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General features for molecule PDB_01300
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_01300
Molecule name [?]:T. TENGCONGENSIS GLMS RIBOZYME WITH G40A MUTATION, BOUND TO GLUCOSAMINE-6-PHOSPHATE
Source [?]:RCSB Protein Data Bank
Source ID [?]:3B4A
Reference [?]:D.J.KLEIN,M.D.BEEN,A.R.FERRE-D'AMARE. ESSENTIAL ROLE OF AN ACTIVE-SITE GUANINE IN GLMS RIBOZYME CATALYSIS.. J.AM.CHEM.SOC. V. 129 14858 2007 ASTM JACSAT US ISSN 0002-7863
Type [?]:Other Ribozyme

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:THERMOANAEROBACTER TENGCONGENSIS
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 2.70 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:142
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:2
Number of unpaired bases [?]:40
Number of paired bases [?]:102

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:27
Maximum length of a stem [?]:10
Average length of a stem [?]:9
Minimum length of a stem [?]:7
Maximum estimated free energy [?]:-11.8
Average estimated free energy [?]:-13
Minimum estimated free energy [?]:-15.1

Hairpin loop features

Number of hairpin loops [?]:2
Maximum number of free bases in hairpin loops [?]:4
Average number of free bases in hairpin loops [?]:3
Minimum number of free bases in hairpin loop [?]:2

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 [?]:1
Maximum number of free bases in internal loops:4
Average number of free bases in internal loops:3
Minimum number of free bases in internal loop:2
Maximum internal loop absolute asymmetry:2
Average internal loop absolute asymmetry:2
Minimum internal loop absolute asymmetry:2
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:2
Minimum internal loop relative asymmetry:2

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 4
Total number of AA non-canonical base pairs:1
Total number of AC non-canonical base pairs:1
Total number of AG non-canonical base pairs:2

Pseudoknot features
Number of pseudoknots [?]:2
Number of bands:4
Number of base pairs in bands:24
Maximum band length:8
Average band length:6
Minimum band length:5
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:1
Average number of un-bands:0.5
Minimum number of un-bands:0
Maximum number of in-bands:1
Average number of in-bands:0.5
Minimum number of in-bands:0
Maximum number of unpaired bases:17
Average number of unpaired bases:11.5
Minimum number of unpaired bases:6
Several ways to remove minimum number of base pairs, per molecule:Yes
Minimum number of base pairs to remove, per molecule:11
Maximum number of base pairs to remove, per pseudoknot:6
Average number of base pairs to remove, per pseudoknot:5.5
Minimum number of base pairs to remove, per pseudoknot:5
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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