Home or other PDB ID
 
 
 
 
 
 
 
 
 
Selection mode
 
 
 
 
 
 
Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA

Results of the assignment of 101 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

Your browser does not support the HTML5 canvas tag.
Your browser does not support the HTML5 canvas tag.
Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.
Define restraints for steps within Å cartesian RMSD, global sigma scaling factor or use per step sigma scaling.
step numberStep nameCANANtCconfalrmsd
0017een_A_OMU1_OMG2AAAAA00670.25 AA00
0027een_A_OMG2_OMC3AAAAA00730.22 AA00
0037een_A_OMC3_OMU4AAAAA00860.17 AA00
0047een_A_OMU4_OMC5AAAAA00810.15 AA00
0057een_A_OMC5_OMC6AAAAA00660.28 AA00
0067een_A_OMC6_OMU7AAAAA00750.33 AA00
0077een_A_OMU7_DA8ZZZZZ01970.14 ZZ01
0087een_A_DA8_DG9NANNANT01.49 BB08
0097een_A_DG9_OMU10OPNOP15680.22 OP15
0107een_A_OMU10_A2M11AAAAA00740.30 AA00
0117een_A_A2M11_OMC12AAAAA08270.48 AA08
0127een_A_OMC12_G13AAAAA00890.24 AA00
0137een_A_G13_A14OPNOP03930.12 OP03
0147een_A_A14_G15AAAAA08630.40 AA08
0157een_A_G15_A16AAAAA00620.25 AA00
0167een_A_A16_G17AAwAA05880.27 AA05
0177een_A_G17_G18AAAAA00290.52 AA00
0187een_A_G18_A19OPNOP08610.20 OP08
0197een_A_A19_C20AAAAA00590.30 AA00
0207een_A_C20_C21AAAAA00430.39 AA00
0217een_A_C21_G22AAAAA00310.47 AA00
0227een_A_G22_G23AAAAA00810.18 AA00
0237een_A_G23_A24AAAAA00830.18 AA00
0247een_A_A24_G25AAAAA00910.10 AA00
0257een_A_G25_U26AAAAA00890.22 AA00
0267een_B_OMU1_OMG2AAAAA00610.25 AA00
0277een_B_OMG2_OMC3AAAAA00730.23 AA00
0287een_B_OMC3_OMU4AAAAA00850.16 AA00
0297een_B_OMU4_OMC5AAAAA00830.16 AA00
0307een_B_OMC5_OMC6AAAAA00630.29 AA00
0317een_B_OMC6_OMU7AAAAA00700.33 AA00
0327een_B_OMU7_DA8ZZZZZ01960.09 ZZ01
0337een_B_DA8_DG9NANNANT01.50 BB08
0347een_B_DG9_OMU10OPNOP15440.27 OP15
0357een_B_OMU10_A2M11AAAAA00640.30 AA00
0367een_B_A2M11_OMC12AAAAA08510.46 AA08
0377een_B_OMC12_G13AAAAA00800.28 AA00
0387een_B_G13_A14OPNOP03860.16 OP03
0397een_B_A14_G15AAAAA08720.42 AA08
0407een_B_G15_A16AAAAA00690.25 AA00
0417een_B_A16_G17AAwAA05890.28 AA05
0427een_B_G17_G18AAAAA00280.47 AA00
0437een_B_G18_A19OPNOP08770.19 OP08
0447een_B_A19_C20AAAAA08660.34 AA08
0457een_B_C20_C21AAAAA00510.40 AA00
0467een_B_C21_G22AAAAA00230.47 AA00
0477een_B_G22_G23AAAAA00780.18 AA00
0487een_B_G23_A24AAAAA00710.15 AA00
0497een_B_A24_G25AAAAA00900.12 AA00
0507een_B_G25_U26AAAAA00910.20 AA00
0517een_B_U26_G27AAAAA08750.35 AA08
0527een_C_OMU1_OMG2AAAAA00700.33 AA00
0537een_C_OMG2_OMC3AAAAA00760.28 AA00
0547een_C_OMC3_OMU4AAAAA00640.20 AA00
0557een_C_OMU4_OMC5AAAAA00430.20 AA00
0567een_C_OMC5_OMC6AAAAA00660.33 AA00
0577een_C_OMC6_OMU7AAAAA00710.30 AA00
0587een_C_OMU7_DA8ZZZZZ01830.19 ZZ01
0597een_C_DA8_DG9NANNANT01.44 BB08
0607een_C_DG9_OMU10OPNOP15580.23 OP15
0617een_C_OMU10_A2M11AAAAA08850.19 AA08
0627een_C_A2M11_OMC12AAAAA08570.48 AA08
0637een_C_OMC12_G13AAAAA00800.32 AA00
0647een_C_G13_A14OPNOP03910.13 OP03
0657een_C_A14_G15AAAAA08750.37 AA08
0667een_C_G15_A16AAAAA00780.23 AA00
0677een_C_A16_G17AAwAA05890.28 AA05
0687een_C_G17_G18AAAAA00180.50 AA00
0697een_C_G18_A19OPNOP08860.13 OP08
0707een_C_A19_C20AAAAA08690.30 AA08
0717een_C_C20_C21AAAAA08750.35 AA08
0727een_C_C21_G22AAAAA00290.45 AA00
0737een_C_G22_G23AAAAA00790.15 AA00
0747een_C_G23_A24AAAAA00740.26 AA00
0757een_C_A24_G25AAwAA01850.16 AA01
0767een_C_G25_U26AAAAA00660.30 AA00
0777een_D_OMU1_OMG2AAuAA12830.25 AA12
0787een_D_OMG2_OMC3AAAAA00530.25 AA00
0797een_D_OMC3_OMU4AAAAA00810.22 AA00
0807een_D_OMU4_OMC5AAAAA00490.20 AA00
0817een_D_OMC5_OMC6AAAAA00710.30 AA00
0827een_D_OMC6_OMU7AAAAA00710.29 AA00
0837een_D_OMU7_DA8ZZZZZ01820.17 ZZ01
0847een_D_DA8_DG9NANNANT01.42 BB08
0857een_D_DG9_OMU10OPNOP15570.23 OP15
0867een_D_OMU10_A2M11AAAAA00710.27 AA00
0877een_D_A2M11_OMC12AAAAA08450.51 AA08
0887een_D_OMC12_G13AAAAA00870.24 AA00
0897een_D_G13_A14OPNOP03690.15 OP03
0907een_D_A14_G15AAAAA08740.38 AA08
0917een_D_G15_A16AAAAA00540.26 AA00
0927een_D_A16_G17AAwAA05870.30 AA05
0937een_D_G17_G18AAAAA00160.45 AA00
0947een_D_G18_A19OPNOP08860.17 OP08
0957een_D_A19_C20AAAAA08670.30 AA08
0967een_D_C20_C21AAAAA00390.41 AA00
0977een_D_C21_G22AAAAA08710.38 AA08
0987een_D_G22_G23AAAAA00770.15 AA00
0997een_D_G23_A24AAAAA00770.27 AA00
1007een_D_A24_G25AAwAA01930.14 AA01
1017een_D_G25_U26AAAAA00710.23 AA00

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
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

Download

Results as csv or json file.
Best NtC fitted to input structure.

Restraints

Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Restraints file for Phenix (steps with RMSD <= 0.5Å) [?]

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of 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).

Browse conformers

Return up to random steps in PDB structures ( include large structures )

Show




Color by conformation group (pyramids)

group
visible

Color by NtC (balls)

A

A-B

B-A

B

IC

OPN

Z

N