Conformers:
ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element
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 34 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 | 1kb4_C_DC401_DA402 | BBB | BB00 | 52 | 0.38 |
| 02 | 1kb4_C_DA402_DC403 | BBB | BB00 | 84 | 0.22 |
| 03 | 1kb4_C_DC403_DA404 | B-A | BA13 | 24 | 0.40 |
| 04 | 1kb4_C_DA404_DG405 | NAN | NANT | 0 | 0.62 |
| 05 | 1kb4_C_DG405_DG406 | BBB | BB00 | 59 | 0.27 |
| 06 | 1kb4_C_DG406_DT407 | NAN | NANT | 0 | 0.21 |
| 07 | 1kb4_C_DT407_DC408 | BBB | BB00 | 38 | 0.28 |
| 08 | 1kb4_C_DC408_DA409 | BB2 | BB07 | 66 | 0.25 |
| 09 | 1kb4_C_DA409_DC410 | BBB | BB00 | 58 | 0.19 |
| 10 | 1kb4_C_DC410_DG411 | B12 | BB04 | 83 | 0.22 |
| 11 | 1kb4_C_DG411_DA412 | BBB | BB00 | 84 | 0.18 |
| 12 | 1kb4_C_DA412_DA413 | B-A | BA13 | 43 | 0.36 |
| 13 | 1kb4_C_DA413_DG414 | A-B | AB01 | 14 | 0.35 |
| 14 | 1kb4_C_DG414_DG415 | BBB | BB00 | 55 | 0.22 |
| 15 | 1kb4_C_DG415_DT416 | BBB | BB00 | 67 | 0.16 |
| 16 | 1kb4_C_DT416_DC417 | BBB | BB00 | 45 | 0.29 |
| 17 | 1kb4_C_DC417_DA418 | B12 | BB04 | 34 | 0.41 |
| 18 | 1kb4_D_DT419_DG420 | BBB | BB00 | 31 | 0.36 |
| 19 | 1kb4_D_DG420_DA421 | BB2 | BB07 | 97 | 0.19 |
| 20 | 1kb4_D_DA421_DC422 | BBB | BB00 | 56 | 0.26 |
| 21 | 1kb4_D_DC422_DC423 | BBB | BB00 | 79 | 0.26 |
| 22 | 1kb4_D_DC423_DT424 | B12 | BB04 | 91 | 0.25 |
| 23 | 1kb4_D_DT424_DT425 | BBw | BB02 | 93 | 0.11 |
| 24 | 1kb4_D_DT425_DC426 | BBB | BB00 | 74 | 0.28 |
| 25 | 1kb4_D_DC426_DG427 | B12 | BB04 | 81 | 0.15 |
| 26 | 1kb4_D_DG427_DT428 | BBw | BB02 | 67 | 0.19 |
| 27 | 1kb4_D_DT428_DG429 | BBB | BB00 | 68 | 0.33 |
| 28 | 1kb4_D_DG429_DA430 | BB2 | BB07 | 83 | 0.28 |
| 29 | 1kb4_D_DA430_DC431 | BBB | BB00 | 68 | 0.27 |
| 30 | 1kb4_D_DC431_DC432 | BBB | BB00 | 76 | 0.21 |
| 31 | 1kb4_D_DC432_DT433 | B12 | BB04 | 82 | 0.25 |
| 32 | 1kb4_D_DT433_DG434 | BBB | BB00 | 88 | 0.16 |
| 33 | 1kb4_D_DG434_DT435 | BBB | BB00 | 83 | 0.31 |
| 34 | 1kb4_D_DT435_DG436 | BBB | BB00 | 63 | 0.20 |
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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