Conformers:
ABBIImiBZICOPNSYNN
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HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA
Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.
Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
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.
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 number | Step name | CANA | NtC | confal | rmsd |
|---|---|---|---|---|---|
| 01 | 1de8_X_DG1_DC2 | B12 | BB05 | 42 | 0.28 |
| 02 | 1de8_X_DC2_DT3 | BBw | BB16 | 74 | 0.26 |
| 03 | 1de8_X_DT3_DA4 | B12 | BB04 | 46 | 0.53 |
| 04 | 1de8_X_DA4_DC5 | BBw | BB11 | 70 | 0.44 |
| 05 | 1de8_X_DG7_DA8 | NAN | NANT | 0 | 0.58 |
| 06 | 1de8_X_DA8_DT9 | BBw | BB02 | 27 | 0.39 |
| 07 | 1de8_X_DT9_DC10 | BBB | BB00 | 76 | 0.26 |
| 08 | 1de8_X_DC10_DG11 | NAN | NANT | 0 | 0.55 |
| 09 | 1de8_Y_DC12_DG13 | BBw | BB03 | 49 | 0.38 |
| 10 | 1de8_Y_DG13_DA14 | BBw | BB11 | 51 | 0.48 |
| 11 | 1de8_Y_DA14_DT15 | NAN | NANT | 0 | 0.72 |
| 12 | 1de8_Y_DT15_DC16 | BB2 | BB07 | 72 | 0.22 |
| 13 | 1de8_Y_DC16_DG17 | NAN | NANT | 0 | 0.71 |
| 14 | 1de8_Y_DG17_DG18 | NAN | NANT | 0 | 0.97 |
| 15 | 1de8_Y_DG18_DT19 | NAN | NANT | 0 | 0.37 |
| 16 | 1de8_Y_DT19_DA20 | BBB | BB00 | 67 | 0.46 |
| 17 | 1de8_Y_DA20_DG21 | BBB | BB00 | 73 | 0.20 |
| 18 | 1de8_Y_DG21_DC22 | BBB | BB00 | 79 | 0.24 |
| 19 | 1de8_U_DG31_DC32 | BBB | BB00 | 21 | 0.29 |
| 20 | 1de8_U_DC32_DT33 | BBB | BB00 | 48 | 0.46 |
| 21 | 1de8_U_DT33_DA34 | B12 | BB04 | 74 | 0.28 |
| 22 | 1de8_U_DA34_DC35 | BBw | BB03 | 64 | 0.52 |
| 23 | 1de8_U_DG37_DA38 | NAN | NANT | 0 | 0.53 |
| 24 | 1de8_U_DA38_DT39 | BBw | BB02 | 82 | 0.16 |
| 25 | 1de8_U_DT39_DC40 | BBB | BB00 | 66 | 0.42 |
| 26 | 1de8_U_DC40_DG41 | NAN | NANT | 0 | 0.62 |
| 27 | 1de8_V_DC42_DG43 | BBw | BB16 | 75 | 0.28 |
| 28 | 1de8_V_DG43_DA44 | BB2 | BB07 | 84 | 0.26 |
| 29 | 1de8_V_DA44_DT45 | BBB | BB00 | 82 | 0.22 |
| 30 | 1de8_V_DT45_DC46 | BB2 | BB07 | 69 | 0.24 |
| 31 | 1de8_V_DC46_DG47 | NAN | NANT | 0 | 0.57 |
| 32 | 1de8_V_DG47_DG48 | NAN | NANT | 0 | 0.84 |
| 33 | 1de8_V_DG48_DT49 | NAN | NANT | 0 | 0.48 |
| 34 | 1de8_V_DT49_DA50 | BBB | BB00 | 41 | 0.48 |
| 35 | 1de8_V_DA50_DG51 | BBw | BB02 | 85 | 0.24 |
| 36 | 1de8_V_DG51_DC52 | BBw | BB03 | 65 | 0.41 |
Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
|
step: Table of conformers |
| δ1 | ε1 | ζ1 | α2 | β2 | γ2 | δ2 | χ1 | χ2 | μ | NN | CC | |
| step_torsions | ||||||||||||
| ntC_average | ||||||||||||
| Δ torsions | ||||||||||||
| torsion scores |
| comments | step 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
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