Home or other PDB ID
 
 
 
 
 
 
 
 
 
Selection mode
 
 
 
 
 
 
Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
APE1 Mn-bound product complex with abasic ribonucleotide DNA

Results of the assignment of 41 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

Your browser does not support the HTML5 canvas tag.
Your browser does not support the HTML5 canvas tag.
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 numberStep nameCANANtCconfalrmsd
017lph_C_DG1_DG2BB2BB07920.26 BB07
027lph_C_DG2_DA3BBBBB00950.14 BB00
037lph_C_DA3_DT4BBBBB01780.23 BB01
047lph_C_DT4_DC5B-ABA05490.24 BA05
057lph_C_DC5_DC6A-BAB03780.21 AB03
067lph_C_DC6_DG7B12BB04870.16 BB04
077lph_C_DG7_DT8BBBBB00530.23 BB00
087lph_C_DT8_DC9BBBBB00700.15 BB00
097lph_C_DC9_DG10B12BB04770.28 BB04
107lph_C_DG10_DA11NANNANT00.41 BB00
117lph_C_DA11_DG12NANNANT00.94 AB02
127lph_C_DG12_DC13NANNANT00.34 BA10
137lph_C_DC13_DG14BBBBB00490.29 BB00
147lph_C_DG14_DC15BBBBB01760.21 BB01
157lph_C_DC15_DA16BBBBB00720.29 BB00
167lph_C_DA16_DT17BBBBB00910.13 BB00
177lph_C_DT17_DC18BBBBB00480.18 BB00
187lph_C_DC18_DA19BBBBB00520.23 BB00
197lph_C_DA19_DG20NANNANT00.29 BA10
207lph_C_DG20_DC21BBBBB01290.43 BB01
217lph_E_DG1_DC2BBBBB01350.32 BB01
227lph_E_DC2_DT3BBBBB00180.32 BB00
237lph_E_DT3_DG4BBBBB00640.28 BB00
247lph_E_DG4_DA5BBBBB00330.28 BB00
257lph_E_DA5_DT6BBBBB01910.16 BB01
267lph_E_DT6_DG7BBBBB00790.16 BB00
277lph_E_DG7_DC8BBBBB00690.21 BB00
287lph_E_DC8_DG.A9BBBBB00290.25 BB00
297lph_E_DC8_DG.B9miBBB10240.25 BB10
307lph_E_DG.A9_DC.A10BBBBB01400.29 BB01
317lph_E_DG.B9_DC.B10B-ABA08170.58 BA08
327lph_A_DC.A2_DG3BB2BB07910.16 BB07
337lph_A_DC.B2_DG3BB2BB07940.16 BB07
347lph_A_DG3_DA4BBBBB00960.14 BB00
357lph_A_DA4_DC5B-ABA05920.22 BA05
367lph_A_DC5_DG6BBBBB00330.33 BB00
377lph_A_DG6_DG7BBBBB00360.31 BB00
387lph_A_DG7_DA8BBBBB00420.46 BB00
397lph_A_DA8_DT9BBBBB00840.20 BB00
407lph_A_DT9_DC10BBBBB00760.19 BB00
417lph_A_DC10_DC11NANNANT00.83 BB02

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep 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

Return up to random steps in PDB structures ( include large structures )

Show




Color by conformation group (pyramids)

group
visible

Color by NtC (balls)

A

A-B

B-A

B

IC

OPN

Z

N