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

©Jiří Černý & Bohdan Schneider

HIV-1 subtype B genomic RNA Dimerization Initiation Site

Results of the assignment of 44 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
011xpe_A_C1_U2AAAAA00950.12AA00
021xpe_A_U2_U3AAAAA00900.15AA00
031xpe_A_U3_G4AAAAA00930.09AA00
041xpe_A_G4_C5AAAAA00940.12AA00
051xpe_A_C5_U6AAAAA00680.44AA00
061xpe_A_U6_G7A-BAB05610.27AB05
071xpe_A_G7_A8NANNANT00.72OP17
081xpe_A_A8_A9A-BAB05550.43AB05
091xpe_A_A9_G10NANNANT00.63OP21
101xpe_A_G10_C11AAAAA00850.13AA00
111xpe_A_C11_G12AAAAA00780.19AA00
121xpe_A_G12_C13AAAAA00900.15AA00
131xpe_A_C13_G14AAAAA00850.11AA00
141xpe_A_G14_C15AAAAA08930.15AA08
151xpe_A_C15_A16AAAAA00920.19AA00
161xpe_A_A16_C17AAAAA00840.20AA00
171xpe_A_C17_G18AAAAA00900.12AA00
181xpe_A_G18_G19AAAAA00810.22AA00
191xpe_A_G19_C20AAAAA00710.21AA00
201xpe_A_C20_A21AAwAA01900.12AA01
211xpe_A_A21_A22AAAAA08930.15AA08
221xpe_A_A22_G23AAAAA00950.16AA00
231xpe_B_C1_U2AAAAA00920.16AA00
241xpe_B_U2_U3AAAAA00950.10AA00
251xpe_B_U3_G4AAAAA08830.17AA08
261xpe_B_G4_C5AAAAA08910.15AA08
271xpe_B_C5_U6AAAAA00700.33AA00
281xpe_B_U6_G7A-BAB05790.24AB05
291xpe_B_G7_A8NANNANT00.67OP17
301xpe_B_A8_A9A-BAB05810.34AB05
311xpe_B_A9_G10NANNANT00.70OP21
321xpe_B_G10_C11AAAAA00860.09AA00
331xpe_B_C11_G12AAAAA00820.17AA00
341xpe_B_G12_C13AAAAA00920.10AA00
351xpe_B_C13_G14AAAAA00770.23AA00
361xpe_B_G14_C15AAAAA00970.12AA00
371xpe_B_C15_A16AAAAA00940.24AA00
381xpe_B_A16_C17AAAAA00920.16AA00
391xpe_B_C17_G18AAAAA00940.12AA00
401xpe_B_G18_G19AAAAA00820.17AA00
411xpe_B_G19_C20AAAAA00950.12AA00
421xpe_B_C20_A21AAAAA00950.11AA00
431xpe_B_A21_A22NANNANT00.27AA04
441xpe_B_A22_G23NANNANT00.34AA04

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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