RNA STRAND molecule page

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

General features for molecule PDB_00127
(click to expand/contract all tables)

Format:

Molecule ID [?]:	PDB_00127
Molecule name [?]:	THE CRYSTAL STRUCTURE OF R(GGUCACAGCCC)2 METAL FREE FORM
Source [?]:	RCSB Protein Data Bank
Source ID [?]:	1KD5
Reference [?]:	V.KACER,S.A.SCARINGE,J.N.SCARSDALE,J.P.RIFE. CRYSTAL STRUCTURES OF R(GGUCACAGCCC)2.. ACTA CRYSTALLOGR.,SECT.D V. 59 423 2003 ASTM ABCRE6 DK ISSN 0907-4449
Type [?]:	Synthetic RNA	[?] PS figure PDF figure Figure from original source
Organism [?]:	SYNTHETIC
Validated by NMR or X-Ray [?]:	Yes
Method for secondary structure determination [?]:	X-RAY, RESOLUTION 1.58 ANGSTROMS; ran through RNAview
Number of molecules [?]:	2
Length [?]:	22
Fragments used [?]:	No
Duplicated sequence [?]:	Molecules in the database with the same sequence: PDB_00125, PDB_00126
Number of domains [?]:	1
Number of unpaired bases [?]:	2
Number of paired bases [?]:	20

Click on any header below for additional features.

Stem features

Number of stems [?]:	1
Number of base pairs in stems [?]:	10
Maximum length of a stem [?]:	10
Average length of a stem [?]:	10
Minimum length of a stem [?]:	10
Maximum estimated free energy [?]:	-11.6
Average estimated free energy [?]:	-11.6
Minimum estimated free energy [?]:	-11.6

Hairpin loop features

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

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

Non-canonical base pairs features

Total number of non-canonical base pairs [?]:	4
Total number of AC non-canonical base pairs:	4

Pseudoknot features