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Conformers: ABBIImiBZICOPNSYNN
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Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimic of Tat protein

Results of the assignment of 280 detected steps in 10 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 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
0012kdq-m10_B_G17_G18NANNANT00.41 AA04
0022kdq-m1_B_G17_G18NANNANT00.37 AA04
0032kdq-m2_B_G17_G18NANNANT00.46 AA04
0042kdq-m3_B_G17_G18AAAAA02110.29 AA02
0052kdq-m4_B_G17_G18NANNANT00.42 AA04
0062kdq-m5_B_G17_G18NANNANT00.45 AA04
0072kdq-m6_B_G17_G18AAAAA02510.19 AA02
0082kdq-m7_B_G17_G18NANNANT00.62 AB04
0092kdq-m8_B_G17_G18NANNANT00.28 AA02
0102kdq-m9_B_G17_G18NANNANT00.42 AA09
0112kdq-m10_B_G18_C19AAAAA04190.38 AA04
0122kdq-m1_B_G18_C19NANNANT00.33 AA04
0132kdq-m2_B_G18_C19AAAAA04220.37 AA04
0142kdq-m3_B_G18_C19AAAAA04220.31 AA04
0152kdq-m4_B_G18_C19NANNANT00.35 AA04
0162kdq-m5_B_G18_C19NANNANT00.37 AA04
0172kdq-m6_B_G18_C19NANNANT00.30 AA04
0182kdq-m7_B_G18_C19NANNANT00.30 AA04
0192kdq-m8_B_G18_C19AAAAA04200.34 AA04
0202kdq-m9_B_G18_C19NANNANT00.32 AA04
0212kdq-m10_B_C19_A20AAAAA04200.58 AA04
0222kdq-m1_B_C19_A20AAAAA04220.58 AA04
0232kdq-m2_B_C19_A20AAAAA04160.59 AA04
0242kdq-m3_B_C19_A20AAAAA04230.54 AA04
0252kdq-m4_B_C19_A20AAAAA04180.60 AA04
0262kdq-m5_B_C19_A20AAAAA04170.59 AA04
0272kdq-m6_B_C19_A20AAAAA04210.60 AA04
0282kdq-m7_B_C19_A20AAAAA04210.59 AA04
0292kdq-m8_B_C19_A20AAAAA04150.58 AA04
0302kdq-m9_B_C19_A20AAAAA04270.58 AA04
0312kdq-m10_B_A20_G21NANNANT00.55 AA04
0322kdq-m1_B_A20_G21NANNANT00.46 AA04
0332kdq-m2_B_A20_G21NANNANT00.68 AA08
0342kdq-m3_B_A20_G21NANNANT00.52 AA04
0352kdq-m4_B_A20_G21NANNANT00.52 AA04
0362kdq-m5_B_A20_G21NANNANT00.67 AA08
0372kdq-m6_B_A20_G21NANNANT00.65 AA08
0382kdq-m7_B_A20_G21NANNANT00.55 AA04
0392kdq-m8_B_A20_G21NANNANT00.57 AA04
0402kdq-m9_B_A20_G21NANNANT00.52 AA04
0412kdq-m10_B_G21_A22NANNANT00.48 AB04
0422kdq-m1_B_G21_A22NANNANT00.37 AB04
0432kdq-m2_B_G21_A22NANNANT00.43 AB04
0442kdq-m3_B_G21_A22NANNANT00.41 AB04
0452kdq-m4_B_G21_A22NANNANT00.57 AB04
0462kdq-m5_B_G21_A22NANNANT00.63 BB16
0472kdq-m6_B_G21_A22NANNANT00.53 AB04
0482kdq-m7_B_G21_A22NANNANT00.46 AB04
0492kdq-m8_B_G21_A22NANNANT00.47 AB04
0502kdq-m9_B_G21_A22NANNANT00.41 AB04
0512kdq-m10_B_A22_U23NANNANT00.65 BA16
0522kdq-m1_B_A22_U23NANNANT00.86 BB02
0532kdq-m2_B_A22_U23NANNANT00.61 BB13
0542kdq-m3_B_A22_U23NANNANT00.68 BB13
0552kdq-m4_B_A22_U23NANNANT01.03 BB02
0562kdq-m5_B_A22_U23NANNANT00.93 BB02
0572kdq-m6_B_A22_U23NANNANT00.73 BB11
0582kdq-m7_B_A22_U23NANNANT00.70 BB13
0592kdq-m8_B_A22_U23NANNANT00.76 BB02
0602kdq-m9_B_A22_U23NANNANT00.75 BB13
0612kdq-m10_B_U23_C24NANNANT01.09 IC03
0622kdq-m1_B_U23_C24NANNANT01.42 OP24
0632kdq-m2_B_U23_C24NANNANT01.09 IC04
0642kdq-m3_B_U23_C24NANNANT01.42 OP23
0652kdq-m4_B_U23_C24NANNANT01.41 OP20
0662kdq-m5_B_U23_C24NANNANT01.19 OP23
0672kdq-m6_B_U23_C24NANNANT01.32 OP23
0682kdq-m7_B_U23_C24NANNANT01.42 IC03
0692kdq-m8_B_U23_C24NANNANT01.53 OP23
0702kdq-m9_B_U23_C24NANNANT02.62 OP27
0712kdq-m10_B_C24_U25NANNANT00.84 OP19
0722kdq-m1_B_C24_U25NANNANT02.09 OP22
0732kdq-m2_B_C24_U25NANNANT02.03 IC01
0742kdq-m3_B_C24_U25NANNANT00.89 OP19
0752kdq-m4_B_C24_U25NANNANT02.04 OP22
0762kdq-m5_B_C24_U25NANNANT02.09 OP22
0772kdq-m6_B_C24_U25NANNANT02.13 IC01
0782kdq-m7_B_C24_U25NANNANT01.37 ZZS2
0792kdq-m8_B_C24_U25NANNANT01.25 ZZS2
0802kdq-m9_B_C24_U25NANNANT01.09 OP19
0812kdq-m10_B_U25_G26NANNANT00.95 OP05
0822kdq-m1_B_U25_G26NANNANT00.98 OP05
0832kdq-m2_B_U25_G26NANNANT01.35 OP06
0842kdq-m3_B_U25_G26NANNANT01.17 OP05
0852kdq-m4_B_U25_G26NANNANT01.17 OP05
0862kdq-m5_B_U25_G26NANNANT01.08 OP06
0872kdq-m6_B_U25_G26NANNANT01.21 OP06
0882kdq-m7_B_U25_G26NANNANT01.24 OP05
0892kdq-m8_B_U25_G26NANNANT01.20 OP05
0902kdq-m9_B_U25_G26NANNANT00.74 OP21
0912kdq-m10_B_G26_A27AAAAA04400.31 AA04
0922kdq-m1_B_G26_A27AAAAA04340.30 AA04
0932kdq-m2_B_G26_A27AAAAA04380.36 AA04
0942kdq-m3_B_G26_A27AAAAA04290.26 AA04
0952kdq-m4_B_G26_A27AAAAA04240.45 AA04
0962kdq-m5_B_G26_A27AAAAA04400.33 AA04
0972kdq-m6_B_G26_A27AAAAA04440.36 AA04
0982kdq-m7_B_G26_A27NANNANT00.42 AA04
0992kdq-m8_B_G26_A27AAAAA04240.37 AA04
1002kdq-m9_B_G26_A27AAAAA04310.30 AA04
1012kdq-m10_B_A27_G28NANNANT00.39 AB04
1022kdq-m1_B_A27_G28AAAAA00130.32 AA00
1032kdq-m2_B_A27_G28AAAAA04490.47 AA04
1042kdq-m3_B_A27_G28AAAAA03240.30 AA03
1052kdq-m4_B_A27_G28AAAAA00100.40 AA00
1062kdq-m5_B_A27_G28AAAAA03320.21 AA03
1072kdq-m6_B_A27_G28AAAAA03230.25 AA03
1082kdq-m7_B_A27_G28AAAAA03230.43 AA03
1092kdq-m8_B_A27_G28AAAAA03250.30 AA03
1102kdq-m9_B_A27_G28AAAAA03200.30 AA03
1112kdq-m10_B_G28_C29NANNANT00.48 AA03
1122kdq-m1_B_G28_C29AAAAA00200.24 AA00
1132kdq-m2_B_G28_C29AAAAA03180.43 AA03
1142kdq-m3_B_G28_C29AAAAA00130.31 AA00
1152kdq-m4_B_G28_C29AAAAA00120.41 AA00
1162kdq-m5_B_G28_C29AAAAA03120.39 AA03
1172kdq-m6_B_G28_C29AAAAA03110.45 AA03
1182kdq-m7_B_G28_C29AAAAA00240.27 AA00
1192kdq-m8_B_G28_C29AAAAA03110.46 AA03
1202kdq-m9_B_G28_C29AAAAA0090.30 AA00
1212kdq-m10_B_C29_C30NANNANT00.42 AA05
1222kdq-m1_B_C29_C30NANNANT00.88 AA10
1232kdq-m2_B_C29_C30NANNANT01.13 AB04
1242kdq-m3_B_C29_C30NANNANT00.85 BA10
1252kdq-m4_B_C29_C30NANNANT00.68 BB16
1262kdq-m5_B_C29_C30NANNANT00.44 AA05
1272kdq-m6_B_C29_C30NANNANT00.86 BB13
1282kdq-m7_B_C29_C30NANNANT01.34 AA04
1292kdq-m8_B_C29_C30NANNANT00.73 AA08
1302kdq-m9_B_C29_C30NANNANT00.69 AA10
1312kdq-m10_B_C30_U31NANNANT00.63 OP09
1322kdq-m1_B_C30_U31NANNANT02.61 BB11
1332kdq-m2_B_C30_U31NANNANT02.48 AB02
1342kdq-m3_B_C30_U31NANNANT00.69 OP09
1352kdq-m4_B_C30_U31NANNANT01.23 OP18
1362kdq-m5_B_C30_U31NANNANT01.59 OP24
1372kdq-m6_B_C30_U31NANNANT00.53 OP09
1382kdq-m7_B_C30_U31NANNANT00.69 BB13
1392kdq-m8_B_C30_U31NANNANT00.87 OP04
1402kdq-m9_B_C30_U31NANNANT00.68 OP09
1412kdq-m10_B_U31_G32NANNANT01.77 OP16
1422kdq-m1_B_U31_G32NANNANT01.78 OP25
1432kdq-m2_B_U31_G32NANNANT01.77 OP26
1442kdq-m3_B_U31_G32NANNANT01.43 BB10
1452kdq-m4_B_U31_G32NANNANT01.10 IC03
1462kdq-m5_B_U31_G32NANNANT01.53 OP17
1472kdq-m6_B_U31_G32NANNANT00.91 OP14
1482kdq-m7_B_U31_G32NANNANT01.68 OP1S
1492kdq-m8_B_U31_G32NANNANT02.07 IC07
1502kdq-m9_B_U31_G32NANNANT01.84 BB1S
1512kdq-m10_B_G32_G33NANNANT02.41 IC03
1522kdq-m1_B_G32_G33NANNANT01.28 OP22
1532kdq-m2_B_G32_G33NANNANT01.33 ZZ2S
1542kdq-m3_B_G32_G33NANNANT01.57 OP17
1552kdq-m4_B_G32_G33NANNANT01.07 OP17
1562kdq-m5_B_G32_G33NANNANT01.18 OP18
1572kdq-m6_B_G32_G33NANNANT02.23 OP28
1582kdq-m7_B_G32_G33NANNANT00.90 OPS1
1592kdq-m8_B_G32_G33NANNANT01.88 ZZS2
1602kdq-m9_B_G32_G33NANNANT02.21 OP1S
1612kdq-m10_B_G33_G34NANNANT01.49 BA09
1622kdq-m1_B_G33_G34NANNANT01.57 OP23
1632kdq-m2_B_G33_G34NANNANT01.33 AB02
1642kdq-m3_B_G33_G34NANNANT01.37 OP28
1652kdq-m4_B_G33_G34NANNANT00.92 OP27
1662kdq-m5_B_G33_G34NANNANT01.72 BB10
1672kdq-m6_B_G33_G34NANNANT01.77 BA09
1682kdq-m7_B_G33_G34NANNANT01.07 BB20
1692kdq-m8_B_G33_G34NANNANT01.00 ZZ01
1702kdq-m9_B_G33_G34NANNANT01.74 OP27
1712kdq-m10_B_G34_A35NANNANT01.77 OP23
1722kdq-m1_B_G34_A35NANNANT01.63 BB1S
1732kdq-m2_B_G34_A35NANNANT01.04 OPS1
1742kdq-m3_B_G34_A35NANNANT02.21 OP25
1752kdq-m4_B_G34_A35NANNANT01.15 OP17
1762kdq-m5_B_G34_A35NANNANT01.13 OP23
1772kdq-m6_B_G34_A35NANNANT02.20 OP27
1782kdq-m7_B_G34_A35NANNANT02.02 OP27
1792kdq-m8_B_G34_A35NANNANT01.14 IC03
1802kdq-m9_B_G34_A35NANNANT01.14 IC06
1812kdq-m10_B_A35_G36NANNANT00.88 OP27
1822kdq-m1_B_A35_G36NANNANT01.62 IC07
1832kdq-m2_B_A35_G36NANNANT00.64 OP27
1842kdq-m3_B_A35_G36NANNANT01.86 OP06
1852kdq-m4_B_A35_G36NANNANT01.90 OP16
1862kdq-m5_B_A35_G36NANNANT01.91 OP16
1872kdq-m6_B_A35_G36NANNANT01.86 OP16
1882kdq-m7_B_A35_G36NANNANT01.62 IC07
1892kdq-m8_B_A35_G36NANNANT00.63 OP27
1902kdq-m9_B_A35_G36NANNANT01.53 OP31
1912kdq-m10_B_G36_C37NANNANT00.69 BB13
1922kdq-m1_B_G36_C37NANNANT00.70 BA09
1932kdq-m2_B_G36_C37NANNANT00.69 AA10
1942kdq-m3_B_G36_C37NANNANT00.61 AA10
1952kdq-m4_B_G36_C37NANNANT00.45 AA11
1962kdq-m5_B_G36_C37NANNANT00.42 AA11
1972kdq-m6_B_G36_C37NANNANT00.33 AA06
1982kdq-m7_B_G36_C37NANNANT00.48 AA06
1992kdq-m8_B_G36_C37NANNANT00.41 AA11
2002kdq-m9_B_G36_C37NANNANT00.41 AA11
2012kdq-m10_B_C37_U38NANNANT00.46 AA03
2022kdq-m1_B_C37_U38NANNANT00.44 AB04
2032kdq-m2_B_C37_U38NANNANT00.36 AB04
2042kdq-m3_B_C37_U38NANNANT00.55 AB04
2052kdq-m4_B_C37_U38AAAAA00110.32 AA00
2062kdq-m5_B_C37_U38NANNANT00.46 AB04
2072kdq-m6_B_C37_U38AAAAA0070.36 AA00
2082kdq-m7_B_C37_U38AAAAA00100.36 AA00
2092kdq-m8_B_C37_U38AAAAA0060.39 AA00
2102kdq-m9_B_C37_U38AAAAA0080.32 AA00
2112kdq-m10_B_U38_C39AAAAA00280.27 AA00
2122kdq-m1_B_U38_C39AAAAA00200.27 AA00
2132kdq-m2_B_U38_C39AAAAA00240.26 AA00
2142kdq-m3_B_U38_C39AAAAA00180.32 AA00
2152kdq-m4_B_U38_C39AAAAA00310.29 AA00
2162kdq-m5_B_U38_C39AAAAA00220.30 AA00
2172kdq-m6_B_U38_C39AAAAA00220.25 AA00
2182kdq-m7_B_U38_C39AAAAA00270.25 AA00
2192kdq-m8_B_U38_C39AAAAA00250.25 AA00
2202kdq-m9_B_U38_C39AAAAA00220.26 AA00
2212kdq-m10_B_C39_U40AAAAA04470.25 AA04
2222kdq-m1_B_C39_U40AAAAA04450.23 AA04
2232kdq-m2_B_C39_U40AAAAA04460.25 AA04
2242kdq-m3_B_C39_U40AAAAA04430.23 AA04
2252kdq-m4_B_C39_U40AAAAA04460.25 AA04
2262kdq-m5_B_C39_U40AAAAA04410.26 AA04
2272kdq-m6_B_C39_U40AAAAA04430.27 AA04
2282kdq-m7_B_C39_U40AAAAA04420.26 AA04
2292kdq-m8_B_C39_U40AAAAA04430.26 AA04
2302kdq-m9_B_C39_U40AAAAA00170.29 AA00
2312kdq-m10_B_U40_C41AAAAA00100.29 AA00
2322kdq-m1_B_U40_C41AAAAA04280.38 AA04
2332kdq-m2_B_U40_C41NANNANT00.38 AB04
2342kdq-m3_B_U40_C41AAAAA00110.33 AA00
2352kdq-m4_B_U40_C41NANNANT00.37 AB04
2362kdq-m5_B_U40_C41AAAAA0090.26 AA00
2372kdq-m6_B_U40_C41NANNANT00.39 AB04
2382kdq-m7_B_U40_C41AAAAA04240.41 AA04
2392kdq-m8_B_U40_C41AAAAA04250.42 AA04
2402kdq-m9_B_U40_C41AAAAA04340.31 AA04
2412kdq-m10_B_C41_U42AAAAA04190.36 AA04
2422kdq-m1_B_C41_U42NANNANT00.54 AA04
2432kdq-m2_B_C41_U42AAAAA04210.31 AA04
2442kdq-m3_B_C41_U42AAAAA04260.47 AA04
2452kdq-m4_B_C41_U42NANNANT00.46 AA04
2462kdq-m5_B_C41_U42AAAAA04210.37 AA04
2472kdq-m6_B_C41_U42AAAAA04130.38 AA04
2482kdq-m7_B_C41_U42NANNANT00.51 AA04
2492kdq-m8_B_C41_U42NANNANT00.50 AA04
2502kdq-m9_B_C41_U42NANNANT00.52 AA04
2512kdq-m10_B_U42_G43AAAAA04140.52 AA04
2522kdq-m1_B_U42_G43NANNANT00.62 AA08
2532kdq-m2_B_U42_G43AAAAA04180.46 AA04
2542kdq-m3_B_U42_G43AAAAA04180.54 AA04
2552kdq-m4_B_U42_G43AAAAA04140.56 AA04
2562kdq-m5_B_U42_G43AAAAA04170.46 AA04
2572kdq-m6_B_U42_G43AAAAA04160.55 AA04
2582kdq-m7_B_U42_G43NANNANT00.56 AA04
2592kdq-m8_B_U42_G43NANNANT00.57 AA04
2602kdq-m9_B_U42_G43NANNANT00.65 AA08
2612kdq-m10_B_G43_C44NANNANT00.32 AB04
2622kdq-m1_B_G43_C44AAAAA04180.37 AA04
2632kdq-m2_B_G43_C44NANNANT00.33 AB04
2642kdq-m3_B_G43_C44NANNANT00.34 AB04
2652kdq-m4_B_G43_C44AAAAA04170.46 AA04
2662kdq-m5_B_G43_C44NANNANT00.31 AB04
2672kdq-m6_B_G43_C44AAAAA0260.42 AA02
2682kdq-m7_B_G43_C44NANNANT00.34 AB04
2692kdq-m8_B_G43_C44NANNANT00.36 AB04
2702kdq-m9_B_G43_C44NANNANT00.34 AB04
2712kdq-m10_B_C44_C45AAAAA02470.23 AA02
2722kdq-m1_B_C44_C45AAAAA04140.61 AA04
2732kdq-m2_B_C44_C45AAAAA04150.61 AA04
2742kdq-m3_B_C44_C45AAAAA04130.56 AA04
2752kdq-m4_B_C44_C45AAAAA04150.55 AA04
2762kdq-m5_B_C44_C45AAAAA04150.56 AA04
2772kdq-m6_B_C44_C45NANNANT00.64 AB03
2782kdq-m7_B_C44_C45AAAAA04100.62 AA04
2792kdq-m8_B_C44_C45AAAAA02270.35 AA02
2802kdq-m9_B_C44_C45AAAAA04150.58 AA04

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

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