Home or other PDB ID
 
 
 
 
 
 
 
 
 
Selection mode
 
 
 
 
 
 
Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate

Results of the assignment of 158 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
0012gdi_X_GTP10_G11AAAAA00640.19 AA00
0022gdi_X_G11_A12AAAAA00860.19 AA00
0032gdi_X_A12_C13AAAAA00830.15 AA00
0042gdi_X_C13_U14AAAAA00340.24 AA00
0052gdi_X_U14_C15AAAAA04640.34 AA04
0062gdi_X_C15_G16AAAAA00570.25 AA00
0072gdi_X_G16_G17AAAAA00720.19 AA00
0082gdi_X_G17_G18AAAAA00920.22 AA00
0092gdi_X_G18_G19AAAAA00330.33 AA00
0102gdi_X_G19_U20AAAAA02490.32 AA02
0112gdi_X_U20_G21NANNANT01.71 OP24
0122gdi_X_G21_C22AAAAA00700.28 AA00
0132gdi_X_C22_C23A-BAB05810.22 AB05
0142gdi_X_C23_C24NANNANT00.45 OP26
0152gdi_X_C24_U25NANNANT00.78 AA04
0162gdi_X_U25_U26AAAAA00790.17 AA00
0172gdi_X_U26_C27AAAAA00900.10 AA00
0182gdi_X_C27_U28ZZZZZ01930.21 ZZ01
0192gdi_X_U28_G29NANNANT00.52 OP25
0202gdi_X_G29_C30AAAAA00520.27 AA00
0212gdi_X_C30_G31AAAAA00440.36 AA00
0222gdi_X_G31_U32AAAAA08870.23 AA08
0232gdi_X_U32_G33AAAAA08780.27 AA08
0242gdi_X_G33_A34AAAAA00890.14 AA00
0252gdi_X_A34_A35AAAAA00900.13 AA00
0262gdi_X_A35_G36AAAAA00520.34 AA00
0272gdi_X_G36_G37AAAAA00860.17 AA00
0282gdi_X_G37_C38AAAAA00320.34 AA00
0292gdi_X_C38_U39AAAAA00850.17 AA00
0302gdi_X_U39_G40AAAAA00740.26 AA00
0312gdi_X_G40_A41OPNOP04930.12 OP04
0322gdi_X_A41_G42AAAAA08680.30 AA08
0332gdi_X_G42_A43ICLIC01640.27 IC01
0342gdi_X_A43_A44NANNANT01.04 OP22
0352gdi_X_A44_A45NANNANT01.56 OP19
0362gdi_X_A45_U46NANNANT00.69 AA02
0372gdi_X_U46_A47NANNANT01.22 BB14
0382gdi_X_A47_C48AAAAA00900.16 AA00
0392gdi_X_C48_C49AAAAA00780.16 AA00
0402gdi_X_C49_C50AAAAA00820.17 AA00
0412gdi_X_C50_G51AAAAA00670.24 AA00
0422gdi_X_G51_U52OPNOP28490.13 OP28
0432gdi_X_U52_A53NANNANT01.33 OP26
0442gdi_X_A53_U54NANNANT00.75 OP29
0452gdi_X_U54_C55NANNANT01.66 IC03
0462gdi_X_C55_A56NANNANT01.77 OP14
0472gdi_X_A56_C57AAAAA08240.68 AA08
0482gdi_X_C57_C58AAAAA00600.15 AA00
0492gdi_X_C58_U59AAAAA00870.18 AA00
0502gdi_X_U59_G60AAAAA00490.36 AA00
0512gdi_X_G60_A61NANNANT00.40 ZZ01
0522gdi_X_A61_U62OPNOP18700.57 OP18
0532gdi_X_U62_C63NANNANT00.69 OP11
0542gdi_X_C63_U64AAAAA00960.17 AA00
0552gdi_X_U64_G65AAAAA00300.24 AA00
0562gdi_X_G65_G66AAAAA00760.16 AA00
0572gdi_X_G66_A67AAAAA00610.16 AA00
0582gdi_X_A67_U68AAAAA00820.23 AA00
0592gdi_X_U68_A69OPNOP04880.16 OP04
0602gdi_X_A69_A70AAAAA00710.29 AA00
0612gdi_X_A70_U71AAAAA00740.23 AA00
0622gdi_X_U71_G72OPNOP04520.40 OP04
0632gdi_X_G72_C73NANNANT00.96 OP30
0642gdi_X_C73_C74AAAAA00790.18 AA00
0652gdi_X_C74_A75AAAAA00730.20 AA00
0662gdi_X_A75_G76AAAAA00760.21 AA00
0672gdi_X_G76_C77AAAAA08650.38 AA08
0682gdi_X_C77_G78ZZZZZ01920.17 ZZ01
0692gdi_X_G78_U79NANNANT00.97 OP21
0702gdi_X_U79_A80NANNANT02.04 OP16
0712gdi_X_A80_G81AAAAA08920.21 AA08
0722gdi_X_G81_G82AAAAA00830.14 AA00
0732gdi_X_G82_G83AAAAA00300.43 AA00
0742gdi_X_G83_A84AAuAA07530.30 AA07
0752gdi_X_A84_A85NANNANT00.63 IC07
0762gdi_X_A85_G86B-ABA17260.51 BA17
0772gdi_X_G86_U87AAAAA00450.23 AA00
0782gdi_X_U87_U88AAAAA08850.19 AA08
0792gdi_X_U88_CCC89AAAAA04370.32 AA04
0802gdi_Y_GTP10_G11AAAAA00650.19 AA00
0812gdi_Y_G11_A12AAAAA00930.13 AA00
0822gdi_Y_A12_C13AAAAA00800.10 AA00
0832gdi_Y_C13_U14AAAAA08810.17 AA08
0842gdi_Y_U14_C15AAAAA04860.31 AA04
0852gdi_Y_C15_G16AAAAA00460.25 AA00
0862gdi_Y_G16_G17AAAAA00600.18 AA00
0872gdi_Y_G17_G18AAAAA00830.23 AA00
0882gdi_Y_G18_G19AAAAA00480.30 AA00
0892gdi_Y_G19_U20AAAAA02480.27 AA02
0902gdi_Y_U20_G21OPNOP01590.52 OP01
0912gdi_Y_G21_C22AAAAA00930.14 AA00
0922gdi_Y_C22_C23A-BAB05870.22 AB05
0932gdi_Y_C23_C24NANNANT00.49 OP26
0942gdi_Y_C24_U25NANNANT00.88 AA12
0952gdi_Y_U25_U26AAAAA00720.23 AA00
0962gdi_Y_U26_C27AAAAA08800.25 AA08
0972gdi_Y_C27_U28ZZZZZ01880.25 ZZ01
0982gdi_Y_U28_G29NANNANT00.49 OP25
0992gdi_Y_G29_C30AAAAA00640.22 AA00
1002gdi_Y_C30_G31AAAAA00600.35 AA00
1012gdi_Y_G31_U32AAAAA00780.30 AA00
1022gdi_Y_U32_G33AAwAA06880.17 AA06
1032gdi_Y_G33_A34AAAAA08590.23 AA08
1042gdi_Y_A34_A35AAAAA00540.15 AA00
1052gdi_Y_A35_G36AAAAA00670.26 AA00
1062gdi_Y_G36_G37AAAAA00610.17 AA00
1072gdi_Y_G37_C38AAAAA00360.35 AA00
1082gdi_Y_C38_U39AAAAA00830.19 AA00
1092gdi_Y_U39_G40AAAAA08780.17 AA08
1102gdi_Y_G40_A41OPNOP04870.15 OP04
1112gdi_Y_A41_G42AAAAA08750.29 AA08
1122gdi_Y_G42_A43ICLIC01160.30 IC01
1132gdi_Y_A43_A44NANNANT01.22 ZZ02
1142gdi_Y_A44_A45NANNANT01.62 OP19
1152gdi_Y_A45_U46NANNANT00.64 AA05
1162gdi_Y_U46_A47NANNANT01.35 BB14
1172gdi_Y_A47_C48AAAAA00710.24 AA00
1182gdi_Y_C48_C49AAAAA00940.14 AA00
1192gdi_Y_C49_C50AAAAA00760.21 AA00
1202gdi_Y_C50_G51AAAAA00570.25 AA00
1212gdi_Y_G51_U52OPNOP28840.17 OP28
1222gdi_Y_U52_A53NANNANT00.81 ZZ1S
1232gdi_Y_A53_U54NANNANT00.98 OP29
1242gdi_Y_U54_C55NANNANT01.64 OP30
1252gdi_Y_C55_A56NANNANT01.60 OPS1
1262gdi_Y_A56_C57AAAAA08270.68 AA08
1272gdi_Y_C57_C58AAAAA08810.23 AA08
1282gdi_Y_C58_U59AAAAA00810.20 AA00
1292gdi_Y_U59_G60AAAAA08700.30 AA08
1302gdi_Y_G60_A61NANNANT00.40 ZZ01
1312gdi_Y_A61_U62OPNOP18420.59 OP18
1322gdi_Y_U62_C63NANNANT00.79 OP11
1332gdi_Y_C63_U64AAAAA00940.11 AA00
1342gdi_Y_U64_G65AAAAA00860.15 AA00
1352gdi_Y_G65_G66AAAAA00890.13 AA00
1362gdi_Y_G66_A67AAAAA00890.11 AA00
1372gdi_Y_A67_U68AAAAA00760.29 AA00
1382gdi_Y_U68_A69OPNOP04690.16 OP04
1392gdi_Y_A69_A70AAAAA00750.26 AA00
1402gdi_Y_A70_U71AAAAA00700.19 AA00
1412gdi_Y_U71_G72OPNOP03350.25 OP03
1422gdi_Y_G72_C73NANNANT01.08 OP30
1432gdi_Y_C73_C74AAAAA00910.13 AA00
1442gdi_Y_C74_A75AAAAA00780.20 AA00
1452gdi_Y_A75_G76AAAAA00910.15 AA00
1462gdi_Y_G76_C77AAAAA00410.39 AA00
1472gdi_Y_C77_G78ZZZZZ01960.16 ZZ01
1482gdi_Y_G78_U79NANNANT00.45 OP21
1492gdi_Y_U79_A80OPNOP11110.58 OP11
1502gdi_Y_A80_G81AAAAA00760.13 AA00
1512gdi_Y_G81_G82AAwAA01860.11 AA01
1522gdi_Y_G82_G83AAAAA00180.48 AA00
1532gdi_Y_G83_A84AAuAA07510.25 AA07
1542gdi_Y_A84_A85NANNANT00.74 IC07
1552gdi_Y_A85_G86NANNANT00.46 BA08
1562gdi_Y_G86_U87AAAAA00570.17 AA00
1572gdi_Y_U87_U88AAAAA08910.18 AA08
1582gdi_Y_U88_CCC89AAAAA00120.23 AA00

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