Conformers:
ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide 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 38 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 | 7lpj_C_DG1_DG2 | BB2 | BB07 | 79 | 0.33 |
| 02 | 7lpj_C_DG2_DA3 | BBB | BB00 | 80 | 0.19 |
| 03 | 7lpj_C_DA3_DT4 | B-A | BA05 | 69 | 0.22 |
| 04 | 7lpj_C_DT4_DC5 | BBB | BB01 | 59 | 0.17 |
| 05 | 7lpj_C_DC5_DC6 | BBB | BB01 | 54 | 0.18 |
| 06 | 7lpj_C_DC6_DG7 | BBB | BB00 | 73 | 0.30 |
| 07 | 7lpj_C_DG7_DT8 | miB | BB15 | 67 | 0.24 |
| 08 | 7lpj_C_DT8_DC9 | BBB | BB00 | 81 | 0.16 |
| 09 | 7lpj_C_DC9_DG10 | B12 | BB04 | 76 | 0.31 |
| 10 | 7lpj_C_DG10_DA11 | BBB | BB00 | 60 | 0.27 |
| 11 | 7lpj_C_DA11_DG12 | NAN | NANT | 0 | 0.84 |
| 12 | 7lpj_C_DG12_DC13 | B-A | BA10 | 61 | 0.27 |
| 13 | 7lpj_C_DC13_DG14 | A-B | AB01 | 71 | 0.21 |
| 14 | 7lpj_C_DG14_DC15 | BBB | BB01 | 75 | 0.24 |
| 15 | 7lpj_C_DC15_DA16 | BBB | BB00 | 44 | 0.35 |
| 16 | 7lpj_C_DA16_DT17 | BBB | BB00 | 63 | 0.20 |
| 17 | 7lpj_C_DT17_DC18 | B-A | BA08 | 76 | 0.42 |
| 18 | 7lpj_C_DC18_DA19 | NAN | NANT | 0 | 0.25 |
| 19 | 7lpj_C_DA19_DG20 | BBw | BB02 | 48 | 0.14 |
| 20 | 7lpj_C_DG20_DC21 | BBB | BB00 | 74 | 0.23 |
| 21 | 7lpj_E_DG1_DC2 | B-A | BA01 | 40 | 0.23 |
| 22 | 7lpj_E_DC2_DT3 | BBB | BB01 | 12 | 0.38 |
| 23 | 7lpj_E_DT3_DG4 | BBB | BB00 | 55 | 0.27 |
| 24 | 7lpj_E_DG4_DA5 | B12 | BB04 | 58 | 0.19 |
| 25 | 7lpj_E_DA5_DT6 | BBB | BB00 | 90 | 0.13 |
| 26 | 7lpj_E_DT6_DG7 | BBB | BB00 | 86 | 0.23 |
| 27 | 7lpj_E_DG7_DC8 | BBB | BB00 | 33 | 0.19 |
| 28 | 7lpj_E_DC8_DG9 | B12 | BB04 | 77 | 0.22 |
| 29 | 7lpj_E_DG9_DC10 | BBB | BB00 | 92 | 0.18 |
| 30 | 7lpj_E_DC12_DG13 | BB2 | BB07 | 46 | 0.34 |
| 31 | 7lpj_E_DG13_DA14 | BBB | BB00 | 77 | 0.23 |
| 32 | 7lpj_E_DA14_DC15 | BBB | BB00 | 84 | 0.24 |
| 33 | 7lpj_E_DC15_DG16 | BB2 | BB07 | 43 | 0.27 |
| 34 | 7lpj_E_DG16_DG17 | B12 | BB04 | 33 | 0.27 |
| 35 | 7lpj_E_DG17_DA18 | BBB | BB00 | 6 | 0.41 |
| 36 | 7lpj_E_DA18_DT19 | BBB | BB00 | 63 | 0.28 |
| 37 | 7lpj_E_DT19_DC20 | miB | BB10 | 36 | 0.34 |
| 38 | 7lpj_E_DC20_DC21 | NAN | NANT | 0 | 0.80 |
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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