RNA STRAND molecule page

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

General features for molecule PDB_00003
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Format:

Molecule ID [?]:	PDB_00003
Molecule name [?]:	PAROMOMYCIN BINDING INDUCES A LOCAL CONFORMATIONAL CHANGE IN THE A SITE OF 16S RRNA, NMR, 20 STRUCTU
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1A3M
Reference [?]:	D.FOURMY,S.YOSHIZAWA,J.D.PUGLISI. PAROMOMYCIN BINDING INDUCES A LOCAL CONFORMATIONAL CHANGE IN THE A-SITE OF 16 S RRNA.. J.MOL.BIOL. V. 277 333 1998 ASTM JMOBAK UK ISSN 0022-2836
Type [?]:	Other RNA	[?] PS figure PDF figure Figure from original source
Organism [?]:	N/A
Validated by NMR or X-Ray [?]:	Yes
Method for secondary structure determination [?]:	NMR; ran through RNAview
Number of molecules [?]:	2
Length [?]:	27
Fragments used [?]:	Yes
Duplicated sequence [?]:	Molecules in the database with the same sequence: PDB_00023, PDB_00189
Number of domains [?]:	1
Number of unpaired bases [?]:	3
Number of paired bases [?]:	24

Click on any header below for additional features.

Stem features

Number of stems [?]:	2
Number of base pairs in stems [?]:	12
Maximum length of a stem [?]:	7
Average length of a stem [?]:	6
Minimum length of a stem [?]:	5
Maximum estimated free energy [?]:	-9.1
Average estimated free energy [?]:	-9.4
Minimum estimated free energy [?]:	-9.7

Hairpin loop features

Number of hairpin loops [?]:	1
Maximum number of free bases in hairpin loops [?]:	2
Average number of free bases in hairpin loops [?]:	2
Minimum number of free bases in hairpin loop [?]:	2

Bulge loop features

Number of bulge loops [?]:	1
Maximum number of free bases in bulge loops [?]:	1
Average number of free bases in bulge loops [?]:	0.5
Minimum number of free bases in bulge loop [?]:	0

Internal loop features

Multi-loop features

Non-canonical base pairs features

Total number of non-canonical base pairs [?]:	2
Total number of AA non-canonical base pairs:	1
Total number of UU non-canonical base pairs:	1

Pseudoknot features