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

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General features for molecule PDB_00421
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00421
Molecule name [?]:CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-A
Source [?]:RCSB Protein Data Bank
Source ID [?]:1GAX
Reference [?]:S.FUKAI,O.NUREKI,S.SEKINE,A.SHIMADA,J.TAO, D.G.VASSYLYEV,S.YOKOYAMA. STRUCTURAL BASIS FOR DOUBLE-SIEVE DISCRIMINATION OF L-VALINE FROM L-ISOLEUCINE AND L-THREONINE BY THE COMPLEX OF TRNA(VAL) AND VALYL-TRNA SYNTHETASE.. CELL V. 103 793 2000 ASTM CELLB5 US ISSN 0092-8674
Type [?]:Transfer RNA

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:THERMUS THERMOPHILUS
Validated by NMR or X-Ray [?]:Yes
Method for secondary structure determination [?]:X-RAY, RESOLUTION 2.90 ANGSTROMS; ran through RNAview
Number of molecules [?]:3
Length [?]:152
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00473
Number of domains [?]:2
Number of unpaired bases [?]:66
Number of paired bases [?]:86

Click on any header below for additional features.

Stem features

Number of stems [?]:8
Number of base pairs in stems [?]:43
Maximum length of a stem [?]:7
Average length of a stem [?]:5.38
Minimum length of a stem [?]:4
Maximum estimated free energy [?]:-7.9
Average estimated free energy [?]:-11.14
Minimum estimated free energy [?]:-19.1

Hairpin loop features

Number of hairpin loops [?]:6
Maximum number of free bases in hairpin loops [?]:7
Average number of free bases in hairpin loops [?]:7
Minimum number of free bases in hairpin loop [?]:7

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

Multi-loop features
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:4
Average number of free bases in multi-loops:1.5
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:4
Average multi-loop absolute asymmetry:2.33
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:2
Average multi-loop relative asymmetry:0.42
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:4
Average number of branches in multi-loops:4
Minimum number of branches in multi-loops:4

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

Pseudoknot features



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