Conformers:
ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain
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 16 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 | 5hnf_L_DA103_DC104 | BBw | BB11 | 46 | 0.55 |
| 02 | 5hnf_L_DC104_DC105 | BBB | BB00 | 57 | 0.35 |
| 03 | 5hnf_L_DC105_DC106 | BBB | BB00 | 90 | 0.22 |
| 04 | 5hnf_L_DC106_DG107 | BB2 | BB07 | 76 | 0.37 |
| 05 | 5hnf_L_DG107_DT108 | B-A | BA05 | 55 | 0.30 |
| 06 | 5hnf_L_DT108_DG109 | A-B | AB01 | 33 | 0.27 |
| 07 | 5hnf_L_DG109_DG110 | BB2 | BB07 | 80 | 0.30 |
| 08 | 5hnf_L_DG110_DA111 | BBB | BB00 | 80 | 0.16 |
| 09 | 5hnf_M_DT201_DC202 | BBB | BB00 | 47 | 0.23 |
| 10 | 5hnf_M_DC202_DC203 | BBB | BB00 | 64 | 0.24 |
| 11 | 5hnf_M_DC203_DA204 | BB2 | BB07 | 86 | 0.17 |
| 12 | 5hnf_M_DA204_DC205 | B12 | BB04 | 73 | 0.31 |
| 13 | 5hnf_M_DC205_DG206 | BBB | BB00 | 71 | 0.44 |
| 14 | 5hnf_M_DG206_DG207 | BB2 | BB07 | 85 | 0.24 |
| 15 | 5hnf_M_DG207_DG208 | BBB | BB00 | 57 | 0.32 |
| 16 | 5hnf_M_DG208_DT209 | BBB | BB00 | 43 | 0.27 |
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
Show
| Color by conformation group (pyramids) | |
|---|---|
| group | |||||||||
| visible |
| Color by NtC (balls) |
|---|
| A | ||||
|---|---|---|---|---|
| A-B | ||||
|---|---|---|---|---|
| B-A | ||||
|---|---|---|---|---|
| B | ||||
|---|---|---|---|---|
| IC | ||||
|---|---|---|---|---|
| OPN | ||||
|---|---|---|---|---|
| Z | ||||
|---|---|---|---|---|
| N | ||||
|---|---|---|---|---|