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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.

©Jiří Černý & Bohdan Schneider

1.8 A X-ray crystal structure of Apramycin complex with RNA fragment GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC containing the human ribosomal decoding A site: RNA construct with 5'-overhang

Results of the assignment of 31 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.
step numberStep nameCANANtCconfalrmsd
012oe8_A_G1_G2AAAAA00570.26AA00
022oe8_A_G2_G3AAAAA00850.13AA00
032oe8_A_G3_C1404AAAAA00890.15AA00
042oe8_A_A14_C15AAAAA08820.21AA08
052oe8_A_C15_C16AAAAA00940.12AA00
062oe8_A_C1404_G1405AAAAA00900.12AA00
072oe8_A_G1405_U1406AAAAA00680.31AA00
082oe8_A_U1406_C1407AAAAA00720.23AA00
092oe8_A_C1407_G1408AAAAA00930.22AA00
102oe8_A_G1408_C1409AAAAA00920.14AA00
112oe8_A_C1409_U1410AAAAA00790.26AA00
122oe8_A_U1410_A1411AAAAA00840.17AA00
132oe8_A_A1411_G1412AAAAA00940.11AA00
142oe8_A_G1412_U1413AAAAA00810.19AA00
152oe8_A_U1413_A14AAAAA00970.12AA00
162oe8_B_C83_G84AAAAA00330.30AA00
172oe8_B_G84_G85AAAAA00910.11AA00
182oe8_B_G85_U86AAAAA00870.18AA00
192oe8_B_U86_A1487AAAAA00800.17AA00
202oe8_B_C98_C99AAAAA00860.14AA00
212oe8_B_A1487_C1488AAAAA00840.13AA00
222oe8_B_C1488_U1489AAAAA00900.14AA00
232oe8_B_U1489_A1490AAAAA00890.12AA00
242oe8_B_A1490_A1491NANNANT00.65OP04
252oe8_B_A1491_A1492NANNANT00.42OPS1
262oe8_B_A1492_A1493NANNANT00.43OP06
272oe8_B_A1493_G1494NANNANT01.02AA08
282oe8_B_G1494_U1495AAAAA00800.26AA00
292oe8_B_U1495_C1496AAAAA08870.27AA08
302oe8_B_C1496_G1497AAAAA00810.09AA00
312oe8_B_G1497_C98AAAAA00830.16AA00

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.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

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).

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