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

©Jiří Černý & Bohdan Schneider

HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA

Results of the assignment of 36 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
011de8_X_DG1_DC2B12BB05420.28BB05
021de8_X_DC2_DT3BBwBB16740.26BB16
031de8_X_DT3_DA4B12BB04460.53BB04
041de8_X_DA4_DC5BBwBB11700.44BB11
051de8_X_DG7_DA8NANNANT00.58BB08
061de8_X_DA8_DT9BBwBB02270.39BB02
071de8_X_DT9_DC10BBBBB00760.26BB00
081de8_X_DC10_DG11NANNANT00.55BB11
091de8_Y_DC12_DG13BBwBB03490.38BB03
101de8_Y_DG13_DA14BBwBB11510.48BB11
111de8_Y_DA14_DT15NANNANT00.72BB02
121de8_Y_DT15_DC16BB2BB07720.22BB07
131de8_Y_DC16_DG17NANNANT00.71BB00
141de8_Y_DG17_DG18NANNANT00.97BB08
151de8_Y_DG18_DT19NANNANT00.37BB02
161de8_Y_DT19_DA20BBBBB00670.46BB00
171de8_Y_DA20_DG21BBBBB00730.20BB00
181de8_Y_DG21_DC22BBBBB00790.24BB00
191de8_U_DG31_DC32BBBBB00210.29BB00
201de8_U_DC32_DT33BBBBB00480.46BB00
211de8_U_DT33_DA34B12BB04740.28BB04
221de8_U_DA34_DC35BBwBB03640.52BB03
231de8_U_DG37_DA38NANNANT00.53BA17
241de8_U_DA38_DT39BBwBB02820.16BB02
251de8_U_DT39_DC40BBBBB00660.42BB00
261de8_U_DC40_DG41NANNANT00.62BB11
271de8_V_DC42_DG43BBwBB16750.28BB16
281de8_V_DG43_DA44BB2BB07840.26BB07
291de8_V_DA44_DT45BBBBB00820.22BB00
301de8_V_DT45_DC46BB2BB07690.24BB07
311de8_V_DC46_DG47NANNANT00.57BB00
321de8_V_DG47_DG48NANNANT00.84BB08
331de8_V_DG48_DT49NANNANT00.48BB02
341de8_V_DT49_DA50BBBBB00410.48BB00
351de8_V_DA50_DG51BBwBB02850.24BB02
361de8_V_DG51_DC52BBwBB03650.41BB03

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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