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Reference RNA structures collected by CompaRNA since February 18, 2009

The following list contains RNA chains automatically extracted from the Protein Data Bank database.

In total 4177 RNA chains from 1935 PDB records have been extracted by CompaRNA. Out of them, 342 RNA chains are valid. RNA chain is considered valid if:

it has a secondary structure
no defects were detected after manual inspection of the PDB structure
it is at least 20 nucleotides long
no RNAs having similar sequence were earlier released from the PDB database

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PDB id

Date

RNA chain id	RNA chain length	Ref 2D		Ref 3D	VValidity of RNA chains. More on that in FAQ (answer 3.2).

2ZM6

2009-04-14

A	1506	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 1PNX_1_A More on that in FAQ (answer 3.2).

2WDN

2009-04-14

A	2807	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2WDL_0_A More on that in FAQ (answer 3.2).
B	119	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 3F1F_2_B More on that in FAQ (answer 3.2).

2WDM

2009-04-14

V	75	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).
W	76	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).
X	11	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
Y	75	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).

2WDL

2009-04-14

A	2807	std	ext	pdb	Valid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
B	119	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 3F1F_2_B More on that in FAQ (answer 3.2).

2WDK

2009-04-14

V	75	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).
W	76	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).
X	11	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
Y	75	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).

2WDI

2009-04-14

A	2807	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2WDL_0_A More on that in FAQ (answer 3.2).
B	119	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 3F1F_2_B More on that in FAQ (answer 3.2).

2WDH

2009-04-14

V	77	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2FMT_1_C More on that in FAQ (answer 3.2).
W	76	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).
X	10	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
Y	75	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).

2WDG

2009-04-14

V	77	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2FMT_1_C More on that in FAQ (answer 3.2).
W	76	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).
X	10	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
Y	75	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 2HGP_3_B More on that in FAQ (answer 3.2).

2KD4

2009-04-07

A	8	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? no * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
B	8	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? no * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

2RP0

2009-03-31

A	27	std	ext	pdb	Valid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

2RP1

2009-03-31

A	27	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 1KPY_1_A More on that in FAQ (answer 3.2).

3DW4

2009-03-24

A	27	std	ext	pdb	Valid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

3FTF

2009-03-24

C	22	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
D	22	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

3FTE

2009-03-24

C	22	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
D	22	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

3DW5

2009-03-24

A	27	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? no * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 3DEG_6_I More on that in FAQ (answer 3.2).

3DVZ

2009-03-24

A	27	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? no * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 3DEG_6_I More on that in FAQ (answer 3.2).

2KBP

2009-03-24

A	12	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
B	12	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

3DW7

2009-03-24

3DW6

2009-03-24

2KFC

2009-03-17

A	36	std	ext	pdb	Valid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

3EQT

2009-03-10

C	8	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
D	8	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

2VUQ

2009-03-10

A	7	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).
B	7	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

3GCA

2009-03-03

A	33	std	ext	pdb	Valid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

3G9Y

2009-03-03

C	6	std	ext	pdb	Invalid RNA chain. * single stranded? yes * structure is continous? yes * sequence longer than 20 nt? no * similar RNA structures deposited earlier in the PDB: None More on that in FAQ (answer 3.2).

3FIN

2009-03-03

A	2852	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? no * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 3D5B_1_A More on that in FAQ (answer 3.2).
B	119	std	ext	pdb	Invalid RNA chain. * single stranded? no * structure is continous? yes * sequence longer than 20 nt? yes * similar RNA structures deposited earlier in the PDB: 3F1F_2_B More on that in FAQ (answer 3.2).

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