Conformers:
ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Crystal Structure of MBD4 Catalytic Domain 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 18 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 | 4dk9_B_DA1_DA2 | NAN | NANT | 0 | 0.97 |
| 02 | 4dk9_B_DA2_DG3 | NAN | NANT | 0 | 0.76 |
| 03 | 4dk9_B_DG3_DA4 | BBB | BB00 | 27 | 0.48 |
| 04 | 4dk9_B_DA4_DC5 | B-A | BA08 | 31 | 0.32 |
| 05 | 4dk9_B_DC5_DG6 | NAN | NANT | 0 | 1.85 |
| 06 | 4dk9_B_DG6_DT7 | B-A | BA17 | 79 | 0.41 |
| 07 | 4dk9_B_DT7_DG8 | A-B | AB03 | 42 | 0.32 |
| 08 | 4dk9_B_DG8_DG9 | B12 | BB04 | 31 | 0.18 |
| 09 | 4dk9_B_DG9_DA10 | BBB | BB00 | 85 | 0.16 |
| 10 | 4dk9_B_DA10_DC11 | NAN | NANT | 0 | 0.48 |
| 11 | 4dk9_C_DT12_DG13 | BBB | BB00 | 7 | 0.69 |
| 12 | 4dk9_C_DG13_DT14 | BBB | BB00 | 60 | 0.23 |
| 13 | 4dk9_C_DT14_DC15 | B12 | BB04 | 39 | 0.36 |
| 14 | 4dk9_C_DC15_DC16 | BBB | BB00 | 8 | 0.20 |
| 15 | 4dk9_C_DC16_DA17 | BB2 | BB07 | 67 | 0.23 |
| 16 | 4dk9_C_DG19_DT20 | B-A | BA05 | 65 | 0.27 |
| 17 | 4dk9_C_DT20_DC21 | B-A | BA05 | 61 | 0.47 |
| 18 | 4dk9_C_DC21_DT22 | NAN | NANT | 0 | 0.35 |
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 | ||||
|---|---|---|---|---|