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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.
Quadruplex structure of an RNA aptamer against bovine prion protein

Results of the assignment of 198 detected steps in 9 model(s), can be also downloaded as csv file. Average confal 0, percentile 0.

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Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.
step numberStep nameCANANtCconfalrmsd
0012rqj-m1_A_G1_G2BB1BB03490.36BB03
0022rqj-m2_A_G1_G2NANNANT00.41BB03
0032rqj-m3_A_G1_G2BB1BB03440.33BB03
0042rqj-m4_A_G1_G2BB1BB03430.32BB03
0052rqj-m5_A_G1_G2BB1BB03590.26BB03
0062rqj-m6_A_G1_G2BB1BB03600.34BB03
0072rqj-m7_A_G1_G2NANNANT00.42BB03
0082rqj-m8_A_G1_G2NANNANT00.62AB02
0092rqj-m9_A_G1_G2BB1BB03470.32BB03
0102rqj-m1_A_G2_A3NANNANT01.24ZZ1S
0112rqj-m2_A_G2_A3NANNANT01.23ZZ1S
0122rqj-m3_A_G2_A3NANNANT01.24ZZ1S
0132rqj-m4_A_G2_A3NANNANT01.23ZZ1S
0142rqj-m5_A_G2_A3NANNANT01.59BB08
0152rqj-m6_A_G2_A3NANNANT01.60BB08
0162rqj-m7_A_G2_A3NANNANT01.24ZZ1S
0172rqj-m8_A_G2_A3NANNANT01.20ZZ1S
0182rqj-m9_A_G2_A3NANNANT01.26ZZ1S
0192rqj-m1_A_A3_G4NANNANT01.03BB1S
0202rqj-m2_A_A3_G4NANNANT01.03BB1S
0212rqj-m3_A_A3_G4NANNANT01.03BB1S
0222rqj-m4_A_A3_G4NANNANT01.04BB1S
0232rqj-m5_A_A3_G4NANNANT01.04BB1S
0242rqj-m6_A_A3_G4NANNANT01.04BB1S
0252rqj-m7_A_A3_G4NANNANT01.02BB1S
0262rqj-m8_A_A3_G4NANNANT01.05BB1S
0272rqj-m9_A_A3_G4NANNANT01.02BB1S
0282rqj-m1_A_G4_G5A-BAB04540.43AB04
0292rqj-m2_A_G4_G5NANNANT00.59AB03
0302rqj-m3_A_G4_G5A-BAB04370.48AB04
0312rqj-m4_A_G4_G5A-BAB04430.40AB04
0322rqj-m5_A_G4_G5A-BAB04530.43AB04
0332rqj-m6_A_G4_G5A-BAB04570.41AB04
0342rqj-m7_A_G4_G5A-BAB04310.45AB04
0352rqj-m8_A_G4_G5NANNANT00.49AB04
0362rqj-m9_A_G4_G5NANNANT00.56AA03
0372rqj-m1_A_G5_A6NANNANT01.52ZZ2S
0382rqj-m2_A_G5_A6NANNANT01.52ZZ2S
0392rqj-m3_A_G5_A6NANNANT01.44ZZ2S
0402rqj-m4_A_G5_A6NANNANT01.50ZZ2S
0412rqj-m5_A_G5_A6NANNANT01.50ZZ2S
0422rqj-m6_A_G5_A6NANNANT01.49ZZ2S
0432rqj-m7_A_G5_A6NANNANT01.42ZZ2S
0442rqj-m8_A_G5_A6NANNANT01.48ZZ2S
0452rqj-m9_A_G5_A6NANNANT01.83BB2S
0462rqj-m1_A_A6_G7NANNANT00.99OPS1
0472rqj-m2_A_A6_G7NANNANT01.34OP19
0482rqj-m3_A_A6_G7NANNANT01.50IC03
0492rqj-m4_A_A6_G7NANNANT00.92OPS1
0502rqj-m5_A_A6_G7NANNANT00.85OPS1
0512rqj-m6_A_A6_G7NANNANT00.95OPS1
0522rqj-m7_A_A6_G7NANNANT01.54IC03
0532rqj-m8_A_A6_G7NANNANT01.54IC03
0542rqj-m9_A_A6_G7NANNANT00.78OPS1
0552rqj-m1_A_G7_G8NANNANT00.45BB03
0562rqj-m2_A_G7_G8NANNANT00.48BB03
0572rqj-m3_A_G7_G8NANNANT00.50BB03
0582rqj-m4_A_G7_G8NANNANT00.46BB03
0592rqj-m5_A_G7_G8NANNANT00.46BB03
0602rqj-m6_A_G7_G8NANNANT00.46BB03
0612rqj-m7_A_G7_G8NANNANT00.50BB03
0622rqj-m8_A_G7_G8NANNANT00.47BB03
0632rqj-m9_A_G7_G8BB1BB03180.42BB03
0642rqj-m1_A_G8_A9NANNANT01.65BB08
0652rqj-m2_A_G8_A9NANNANT01.65BB08
0662rqj-m3_A_G8_A9NANNANT01.67BB08
0672rqj-m4_A_G8_A9NANNANT01.64BB08
0682rqj-m5_A_G8_A9NANNANT01.63BB08
0692rqj-m6_A_G8_A9NANNANT01.64BB08
0702rqj-m7_A_G8_A9NANNANT01.67BB08
0712rqj-m8_A_G8_A9NANNANT01.67BB08
0722rqj-m9_A_G8_A9NANNANT01.63BB08
0732rqj-m1_A_A9_G10NANNANT01.00OP12
0742rqj-m2_A_A9_G10NANNANT00.91OP12
0752rqj-m3_A_A9_G10NANNANT00.90OP12
0762rqj-m4_A_A9_G10NANNANT00.97OP12
0772rqj-m5_A_A9_G10NANNANT01.02OP12
0782rqj-m6_A_A9_G10NANNANT00.94OP12
0792rqj-m7_A_A9_G10NANNANT00.96OP12
0802rqj-m8_A_A9_G10NANNANT00.91OP12
0812rqj-m9_A_A9_G10NANNANT00.96OP12
0822rqj-m1_A_G10_G11NANNANT00.38AA03
0832rqj-m2_A_G10_G11AA2AA12280.60AA12
0842rqj-m3_A_G10_G11AA2AA12300.57AA12
0852rqj-m4_A_G10_G11AAAAA03410.32AA03
0862rqj-m5_A_G10_G11AAAAA08120.40AA08
0872rqj-m6_A_G10_G11AAAAA03320.29AA03
0882rqj-m7_A_G10_G11AAAAA00250.44AA00
0892rqj-m8_A_G10_G11AAAAA08120.49AA08
0902rqj-m9_A_G10_G11AAAAA00210.43AA00
0912rqj-m1_A_G11_A12NANNANT00.72AA10
0922rqj-m2_A_G11_A12NANNANT00.90ZZ01
0932rqj-m3_A_G11_A12NANNANT00.93ZZ01
0942rqj-m4_A_G11_A12NANNANT00.94ZZ01
0952rqj-m5_A_G11_A12NANNANT00.79AA06
0962rqj-m6_A_G11_A12NANNANT00.74AA10
0972rqj-m7_A_G11_A12NANNANT00.92ZZ01
0982rqj-m8_A_G11_A12NANNANT00.91ZZ01
0992rqj-m9_A_G11_A12NANNANT00.93ZZ01
1002rqj-m1_B_G13_G14BB1BB03630.31BB03
1012rqj-m2_B_G13_G14BB1BB03530.29BB03
1022rqj-m3_B_G13_G14BB1BB03570.31BB03
1032rqj-m4_B_G13_G14BB1BB03270.40BB03
1042rqj-m5_B_G13_G14BB1BB03390.38BB03
1052rqj-m6_B_G13_G14BB1BB03610.27BB03
1062rqj-m7_B_G13_G14BB1BB03570.30BB03
1072rqj-m8_B_G13_G14NANNANT00.39BB03
1082rqj-m9_B_G13_G14BB1BB03670.32BB03
1092rqj-m1_B_G14_A15NANNANT01.60BB08
1102rqj-m2_B_G14_A15NANNANT01.24ZZ1S
1112rqj-m3_B_G14_A15NANNANT01.22ZZ1S
1122rqj-m4_B_G14_A15NANNANT01.23ZZ1S
1132rqj-m5_B_G14_A15NANNANT01.25ZZ1S
1142rqj-m6_B_G14_A15NANNANT01.61BB08
1152rqj-m7_B_G14_A15NANNANT01.58BB08
1162rqj-m8_B_G14_A15NANNANT01.22ZZ1S
1172rqj-m9_B_G14_A15NANNANT01.60BB08
1182rqj-m1_B_A15_G16NANNANT01.04BB1S
1192rqj-m2_B_A15_G16NANNANT01.04BB1S
1202rqj-m3_B_A15_G16NANNANT01.04BB1S
1212rqj-m4_B_A15_G16NANNANT01.02BB1S
1222rqj-m5_B_A15_G16NANNANT01.03BB1S
1232rqj-m6_B_A15_G16NANNANT01.09AAS1
1242rqj-m7_B_A15_G16NANNANT01.05BB1S
1252rqj-m8_B_A15_G16NANNANT01.03BB1S
1262rqj-m9_B_A15_G16NANNANT01.04BB1S
1272rqj-m1_B_G16_G17A-BAB04540.41AB04
1282rqj-m2_B_G16_G17A-BAB04500.39AB04
1292rqj-m3_B_G16_G17A-BAB04340.43AB04
1302rqj-m4_B_G16_G17NANNANT00.46AB04
1312rqj-m5_B_G16_G17A-BAB04450.49AB04
1322rqj-m6_B_G16_G17A-BAB04520.33AB04
1332rqj-m7_B_G16_G17A-BAB04560.42AB04
1342rqj-m8_B_G16_G17NANNANT00.58AB03
1352rqj-m9_B_G16_G17A-BAB04550.42AB04
1362rqj-m1_B_G17_A18NANNANT01.50ZZ2S
1372rqj-m2_B_G17_A18NANNANT01.51ZZ2S
1382rqj-m3_B_G17_A18NANNANT01.45ZZ2S
1392rqj-m4_B_G17_A18NANNANT01.37ZZ2S
1402rqj-m5_B_G17_A18NANNANT01.48ZZ2S
1412rqj-m6_B_G17_A18NANNANT01.42ZZ2S
1422rqj-m7_B_G17_A18NANNANT01.46ZZ2S
1432rqj-m8_B_G17_A18NANNANT01.48ZZ2S
1442rqj-m9_B_G17_A18NANNANT01.50ZZ2S
1452rqj-m1_B_A18_G19NANNANT00.94OPS1
1462rqj-m2_B_A18_G19NANNANT00.88OPS1
1472rqj-m3_B_A18_G19NANNANT00.95OPS1
1482rqj-m4_B_A18_G19NANNANT01.50IC03
1492rqj-m5_B_A18_G19NANNANT01.79IC04
1502rqj-m6_B_A18_G19NANNANT00.91OPS1
1512rqj-m7_B_A18_G19NANNANT00.91OPS1
1522rqj-m8_B_A18_G19NANNANT00.92OPS1
1532rqj-m9_B_A18_G19NANNANT00.97OPS1
1542rqj-m1_B_G19_G20NANNANT00.50BB03
1552rqj-m2_B_G19_G20NANNANT00.47BB03
1562rqj-m3_B_G19_G20NANNANT00.49BB03
1572rqj-m4_B_G19_G20NANNANT00.49BB03
1582rqj-m5_B_G19_G20NANNANT00.52BB03
1592rqj-m6_B_G19_G20NANNANT00.45BB03
1602rqj-m7_B_G19_G20NANNANT00.48BB03
1612rqj-m8_B_G19_G20NANNANT00.47BB03
1622rqj-m9_B_G19_G20NANNANT00.49BB03
1632rqj-m1_B_G20_A21NANNANT01.63BB08
1642rqj-m2_B_G20_A21NANNANT01.64BB08
1652rqj-m3_B_G20_A21NANNANT01.65BB08
1662rqj-m4_B_G20_A21NANNANT01.65BB08
1672rqj-m5_B_G20_A21NANNANT01.65BB08
1682rqj-m6_B_G20_A21NANNANT01.65BB08
1692rqj-m7_B_G20_A21NANNANT01.66BB08
1702rqj-m8_B_G20_A21NANNANT01.65BB08
1712rqj-m9_B_G20_A21NANNANT01.66BB08
1722rqj-m1_B_A21_G22NANNANT01.01OP12
1732rqj-m2_B_A21_G22NANNANT01.03OP12
1742rqj-m3_B_A21_G22NANNANT00.95OP12
1752rqj-m4_B_A21_G22NANNANT00.95OP12
1762rqj-m5_B_A21_G22NANNANT00.97OP12
1772rqj-m6_B_A21_G22NANNANT01.00OP12
1782rqj-m7_B_A21_G22NANNANT00.92OP12
1792rqj-m8_B_A21_G22NANNANT00.96OP12
1802rqj-m9_B_A21_G22NANNANT00.93OP12
1812rqj-m1_B_G22_G23AAAAA08160.34AA08
1822rqj-m2_B_G22_G23AAAAA08140.32AA08
1832rqj-m3_B_G22_G23AA2AA12300.60AA12
1842rqj-m4_B_G22_G23AAAAA08120.43AA08
1852rqj-m5_B_G22_G23AA2AA12250.61AA12
1862rqj-m6_B_G22_G23AAAAA08170.41AA08
1872rqj-m7_B_G22_G23AAAAA00160.48AA00
1882rqj-m8_B_G22_G23AAAAA08170.46AA08
1892rqj-m9_B_G22_G23AAAAA00190.45AA00
1902rqj-m1_B_G23_A24AA1AA0590.61AA05
1912rqj-m2_B_G23_A24NANNANT00.69AA04
1922rqj-m3_B_G23_A24NANNANT00.94ZZ01
1932rqj-m4_B_G23_A24NANNANT00.70AA06
1942rqj-m5_B_G23_A24NANNANT00.98ZZ01
1952rqj-m6_B_G23_A24NANNANT00.70AA06
1962rqj-m7_B_G23_A24NANNANT00.89ZZ01
1972rqj-m8_B_G23_A24NANNANT00.94ZZ01
1982rqj-m9_B_G23_A24NANNANT00.92ZZ01

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.

© Jiří Černý & Bohdan Schneider

Definition of torsion angles
step:
Table of conformers

δεζα1β1γ1δ1χχ1NCCNNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Drag the plot for panning, scroll to zoom, click a point to show superposition in JSmol.

Download

Results (as csv)
Restraints (default edits file)
Best NtC fitted to input structure.

Definition of the conformers as torsion averages (csv) and their esd values (csv) or as their Cartesian coordinates of the conformers

Download the papers:

description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
example of application:
Schneider et al., Genes, 8(10), 278, (2017).

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Color by conformation group (pyramids)

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Color by NtC (balls)

A

A-B

B-A

B

IC

OPN

Z

N