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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.

©Jiří Černý & Bohdan Schneider

Complex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site.

Results of the assignment of 40 detected steps in 1 model(s), can be also downloaded as csv or json 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
012be0_A_G1_C2AAwAA01690.30AA01
022be0_A_C2_G3AAAAA08900.22AA08
032be0_A_G3_U4AAAAA00840.29AA00
042be0_A_U4_C5AAAAA00860.18AA00
052be0_A_C5_A6AAAAA00970.14AA00
062be0_A_A6_C7AAAAA00870.19AA00
072be0_A_C7_A8AAAAA08930.10AA08
082be0_A_A8_C9AAAAA00930.13AA00
092be0_A_C9_C10AAAAA00760.15AA00
102be0_A_C10_G11AAAAA00820.14AA00
112be0_A_G11_G12AAAAA00770.14AA00
122be0_A_G12_U13AAAAA00790.13AA00
132be0_A_U13_G14AAAAA00810.18AA00
142be0_A_G14_A15NANNANT01.95IC01
152be0_A_A15_A16NANNANT00.47AA06
162be0_A_A16_G17NANNANT00.93OP11
172be0_A_G17_U18NANNANT00.67AA12
182be0_A_U18_C19AAAAA08810.20AA08
192be0_A_C19_G20AAAAA00660.25AA00
202be0_A_G20_C21AAwAA01680.24AA01
212be0_B_G22_C23AAwAA01710.30AA01
222be0_B_C23_G24AAAAA08860.21AA08
232be0_B_G24_U25AAAAA00830.27AA00
242be0_B_U25_C26AAAAA00820.20AA00
252be0_B_C26_A27AAAAA00960.17AA00
262be0_B_A27_C28AAAAA00870.20AA00
272be0_B_C28_A29AAAAA00790.14AA00
282be0_B_A29_C30AAAAA00810.15AA00
292be0_B_C30_C31AAAAA00770.18AA00
302be0_B_C31_G32AAAAA00910.14AA00
312be0_B_G32_G33AAAAA00830.12AA00
322be0_B_G33_U34AAAAA00840.14AA00
332be0_B_U34_G35AAAAA00660.20AA00
342be0_B_G35_A36NANNANT01.82OP17
352be0_B_A36_A37NANNANT00.51AA06
362be0_B_A37_G38NANNANT00.91OP11
372be0_B_G38_U39NANNANT00.65AA12
382be0_B_U39_C40AAAAA08830.18AA08
392be0_B_C40_G41AAAAA00820.21AA00
402be0_B_G41_C42AAwAA01700.28AA01

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.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

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).

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