Conformers:
ABBIImiBZICOPNSYNN
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Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit
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 46 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 | 1r3e_C_C404_U405 | AAA | AA00 | 74 | 0.18 |
| 02 | 1r3e_C_U405_G406 | AAA | AA00 | 86 | 0.15 |
| 03 | 1r3e_C_G406_U407 | AAA | AA08 | 78 | 0.20 |
| 04 | 1r3e_C_U407_G408 | AAA | AA00 | 69 | 0.31 |
| 05 | 1r3e_C_G408_U409 | NAN | NANT | 0 | 0.45 |
| 06 | 1r3e_C_C411_G412 | NAN | NANT | 0 | 0.44 |
| 07 | 1r3e_C_G412_A413 | NAN | NANT | 0 | 1.06 |
| 08 | 1r3e_C_A413_U414 | NAN | NANT | 0 | 0.93 |
| 09 | 1r3e_C_U414_C415 | A-B | AB04 | 63 | 0.35 |
| 10 | 1r3e_C_C415_C416 | OPN | OP12 | 53 | 0.18 |
| 11 | 1r3e_C_C416_A417 | AAA | AA00 | 94 | 0.16 |
| 12 | 1r3e_C_A417_C418 | AAA | AA00 | 84 | 0.17 |
| 13 | 1r3e_C_C418_A419 | AAA | AA00 | 97 | 0.11 |
| 14 | 1r3e_C_A419_G420 | AAA | AA00 | 92 | 0.13 |
| 15 | 1r3e_D_C404_U405 | AAA | AA00 | 75 | 0.20 |
| 16 | 1r3e_D_U405_G406 | AAA | AA00 | 88 | 0.16 |
| 17 | 1r3e_D_G406_U407 | AAA | AA00 | 71 | 0.22 |
| 18 | 1r3e_D_U407_G408 | NAN | NANT | 0 | 0.47 |
| 19 | 1r3e_D_G408_U409 | NAN | NANT | 0 | 0.92 |
| 20 | 1r3e_D_U409_U410 | NAN | NANT | 0 | 1.58 |
| 21 | 1r3e_D_U410_C411 | NAN | NANT | 0 | 1.76 |
| 22 | 1r3e_D_C411_G412 | NAN | NANT | 0 | 1.65 |
| 23 | 1r3e_D_G412_A413 | AAA | AA00 | 29 | 0.31 |
| 24 | 1r3e_D_A413_U414 | AAA | AA00 | 79 | 0.26 |
| 25 | 1r3e_D_U414_C415 | AAA | AA00 | 76 | 0.22 |
| 26 | 1r3e_D_C415_C416 | AAw | AA01 | 92 | 0.15 |
| 27 | 1r3e_D_C416_A417 | AAA | AA08 | 86 | 0.25 |
| 28 | 1r3e_D_A417_C418 | AAA | AA00 | 93 | 0.13 |
| 29 | 1r3e_D_C418_A419 | AAA | AA00 | 97 | 0.13 |
| 30 | 1r3e_D_A419_G420 | AAA | AA00 | 94 | 0.13 |
| 31 | 1r3e_E_C404_U405 | AAA | AA00 | 81 | 0.21 |
| 32 | 1r3e_E_U405_G406 | AAw | AA01 | 95 | 0.08 |
| 33 | 1r3e_E_G406_U407 | AAw | AA06 | 88 | 0.24 |
| 34 | 1r3e_E_U407_G408 | AAA | AA08 | 24 | 0.28 |
| 35 | 1r3e_E_G408_U409 | NAN | NANT | 0 | 1.27 |
| 36 | 1r3e_E_U409_U410 | NAN | NANT | 0 | 1.33 |
| 37 | 1r3e_E_U410_C411 | NAN | NANT | 0 | 2.36 |
| 38 | 1r3e_E_C411_G412 | NAN | NANT | 0 | 2.33 |
| 39 | 1r3e_E_G412_A413 | AAA | AA08 | 55 | 0.27 |
| 40 | 1r3e_E_A413_U414 | AAA | AA00 | 78 | 0.22 |
| 41 | 1r3e_E_U414_C415 | AAw | AA01 | 92 | 0.11 |
| 42 | 1r3e_E_C415_C416 | AAA | AA08 | 84 | 0.15 |
| 43 | 1r3e_E_C416_A417 | AAA | AA00 | 76 | 0.21 |
| 44 | 1r3e_E_A417_C418 | AAw | AA01 | 85 | 0.16 |
| 45 | 1r3e_E_C418_A419 | AAw | AA11 | 74 | 0.32 |
| 46 | 1r3e_E_A419_G420 | AAw | AA01 | 30 | 0.44 |
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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| Color by NtC (balls) |
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| A-B | ||||
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| B | ||||
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