Home or other PDB ID
 
 
 
 
 
 
 
 
 
Selection mode
 
 
 
 
 
 
Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
CRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH BOTH EXONS

Results of the assignment of 219 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
0011u6b_B_GTP1_G5AAwAA01340.32 AA01
0021u6b_B_G5_C6AAwAA11910.25 AA11
0031u6b_B_C6_C7AAAAA08110.40 AA08
0041u6b_B_C7_G8AAwAA01700.15 AA01
0051u6b_B_G8_U9AAAAA00410.29 AA00
0061u6b_B_U9_G10AAAAA08780.19 AA08
0071u6b_B_G10_U11AAAAA00630.24 AA00
0081u6b_B_U11_G12AAAAA00800.17 AA00
0091u6b_B_G12_C13AAAAA00750.23 AA00
0101u6b_B_C13_C14AAAAA08880.27 AA08
0111u6b_B_C14_U15AAAAA00910.11 AA00
0121u6b_B_U15_U16AAAAA00830.20 AA00
0131u6b_B_U16_G17AAAAA08920.20 AA08
0141u6b_B_G17_C18AAAAA00790.14 AA00
0151u6b_B_C18_G19AAAAA00690.18 AA00
0161u6b_B_G19_C20AAAAA00810.25 AA00
0171u6b_B_C20_C21NANNANT01.15 AA13
0181u6b_B_C21_G22NANNANT01.35 AA04
0191u6b_B_G22_G23AAAAA00190.35 AA00
0201u6b_B_G23_G24AAAAA00720.33 AA00
0211u6b_B_G24_A25OPNOP03270.17 OP03
0221u6b_B_A25_A26AAAAA08320.31 AA08
0231u6b_B_A26_A27AAAAA04780.24 AA04
0241u6b_B_A27_C28AAAAA08230.67 AA08
0251u6b_B_C28_C29AAwAA06350.28 AA06
0261u6b_B_C29_A30AAAAA08600.31 AA08
0271u6b_B_A30_C31AAAAA08700.18 AA08
0281u6b_B_C31_G32AAAAA00680.16 AA00
0291u6b_B_G32_C33AAAAA04610.30 AA04
0301u6b_B_C33_A34AAAAA08780.22 AA08
0311u6b_B_A34_A35AAAAA08840.19 AA08
0321u6b_B_A35_G36AAAAA00420.23 AA00
0331u6b_B_G36_G37NANNANT00.58 AA06
0341u6b_B_G37_G38NANNANT00.97 AA13
0351u6b_B_G38_A39AAAAA00510.28 AA00
0361u6b_B_A39_U40A-BAB05440.29 AB05
0371u6b_B_U40_G41NANNANT01.89 OP31
0381u6b_B_G41_G42AAAAA00690.23 AA00
0391u6b_B_G42_U43AAAAA00790.18 AA00
0401u6b_B_U43_G44AAAAA00740.17 AA00
0411u6b_B_G44_U45AAAAA00800.14 AA00
0421u6b_B_U45_C46AAAAA00500.26 AA00
0431u6b_B_C46_A47NANNANT00.40 AA02
0441u6b_B_A47_A48NANNANT00.69 OP15
0451u6b_B_A48_A49AAAAA08570.27 AA08
0461u6b_B_A49_U50AAwAA05220.40 AA05
0471u6b_B_U50_U51NANNANT00.57 OP01
0481u6b_B_U51_C52AAAAA00890.15 AA00
0491u6b_B_C52_G53AAwAA10880.26 AA10
0501u6b_B_G53_G54AAAAA08790.16 AA08
0511u6b_B_G54_C55AAAAA00640.26 AA00
0521u6b_B_C55_G56AAAAA00560.36 AA00
0531u6b_B_G56_A57NANNANT00.42 AA10
0541u6b_B_A57_A58AAuAA07770.29 AA07
0551u6b_B_A58_A59AAAAA08500.29 AA08
0561u6b_B_A59_C60AAAAA00300.48 AA00
0571u6b_B_C60_C61AAAAA00520.31 AA00
0581u6b_B_C61_U62AAAAA00910.20 AA00
0591u6b_B_U62_A63NANNANT00.55 AB04
0601u6b_B_A63_A64OPNOP26260.43 OP26
0611u6b_B_A64_G65AAAAA00420.40 AA00
0621u6b_B_G65_C66AAAAA00840.20 AA00
0631u6b_B_C66_G67AAAAA00900.11 AA00
0641u6b_B_G67_C68AAAAA00890.10 AA00
0651u6b_B_C68_C69AAAAA00790.18 AA00
0661u6b_B_C69_C70AAAAA00770.21 AA00
0671u6b_B_C70_G71NANNANT02.30 OP01
0681u6b_B_G71_C72NANNANT00.75 AA12
0691u6b_B_C72_C73NANNANT00.53 AA08
0701u6b_B_C73_C74AAAAA00610.37 AA00
0711u6b_B_C74_G75AAwAA05670.38 AA05
0721u6b_B_G75_G76NANNANT00.57 AA11
0731u6b_B_G76_G77AAAAA08810.21 AA08
0741u6b_B_G77_C78AAAAA00600.21 AA00
0751u6b_B_C78_G79AAAAA00880.21 AA00
0761u6b_B_G79_U80AAAAA08830.21 AA08
0771u6b_B_U80_A81NANNANT00.75 AB05
0781u6b_B_A81_U82NANNANT01.38 AA07
0791u6b_B_U82_G83NANNANT00.86 OP12
0801u6b_B_G83_G84AAwAA01760.22 AA01
0811u6b_B_G84_C85AAAAA03530.23 AA03
0821u6b_B_C85_A86AAAAA04430.55 AA04
0831u6b_B_A86_A87AAuAA12760.38 AA12
0841u6b_B_A87_C88AAwAA05620.31 AA05
0851u6b_B_C88_G89AAuAA12590.40 AA12
0861u6b_B_G89_C90AAwAA10330.26 AA10
0871u6b_B_C90_C91AAAAA08600.29 AA08
0881u6b_B_C91_G92AAAAA00330.32 AA00
0891u6b_B_G92_A93AAAAA00910.16 AA00
0901u6b_B_A93_G94AAAAA00690.24 AA00
0911u6b_B_G94_C95AAAAA00770.19 AA00
0921u6b_B_C95_C96AAAAA00840.21 AA00
0931u6b_B_C96_A97AAuAA12540.48 AA12
0941u6b_B_A97_A98AAAAA00700.23 AA00
0951u6b_B_A98_G99AAAAA00750.33 AA00
0961u6b_B_G99_C100AAwAA06840.17 AA06
0971u6b_B_C100_U101NANNANT00.69 AA03
0981u6b_B_U101_U102AAAAA00880.21 AA00
0991u6b_B_U102_C103AAwAA01370.26 AA01
1001u6b_B_C103_G104AAwAA10110.44 AA10
1011u6b_B_G104_C105AAAAA08720.27 AA08
1021u6b_B_C105_A106AAAAA00940.09 AA00
1031u6b_B_A106_G107NANNANT00.24 AA03
1041u6b_B_G107_C1001AAAAA00750.21 AA00
1051u6b_B_C112_U113NANNANT01.40 OP24
1061u6b_B_U113_G114AAAAA08230.45 AA08
1071u6b_B_G114_C115AAwAA11570.36 AA11
1081u6b_B_C115_G116AAAAA00120.45 AA00
1091u6b_B_G116_A117AAAAA08830.19 AA08
1101u6b_B_A117_U118AAwAA01670.17 AA01
1111u6b_B_U118_G119AAAAA08710.24 AA08
1121u6b_B_G119_A120AAAAA00850.16 AA00
1131u6b_B_A120_A121NANNANT00.18 AA10
1141u6b_B_A121_G122AAAAA08460.51 AA08
1151u6b_B_G122_G123AAAAA00280.30 AA00
1161u6b_B_G123_U124AAAAA08810.17 AA08
1171u6b_B_U124_G125AAAAA08530.52 AA08
1181u6b_B_G125_U126NANNANT00.27 ZZ01
1191u6b_B_U126_A127NANNANT02.07 IC02
1201u6b_B_A127_G128NANNANT01.04 AA13
1211u6b_B_G128_A129NANNANT00.82 IC07
1221u6b_B_A129_G130NANNANT00.78 AA10
1231u6b_B_G130_A131AAAAA04310.50 AA04
1241u6b_B_A131_C132AAAAA04880.15 AA04
1251u6b_B_C132_U133AAAAA00620.22 AA00
1261u6b_B_U133_A134AAAAA08250.31 AA08
1271u6b_B_A134_G135NANNANT00.30 AB2S
1281u6b_B_G135_A136NANNANT00.54 AAS1
1291u6b_B_A136_C137NANNANT00.88 OP25
1301u6b_B_C137_G138NANNANT01.14 OP16
1311u6b_B_G138_G139AAAAA08150.32 AA08
1321u6b_B_G139_C140AAAAA00900.23 AA00
1331u6b_B_C140_A141AAAAA00830.15 AA00
1341u6b_B_A141_C142AAAAA00760.14 AA00
1351u6b_B_C142_C143AAAAA00920.11 AA00
1361u6b_B_C143_C144AAAAA00800.15 AA00
1371u6b_B_C144_A145AAAAA00660.21 AA00
1381u6b_B_A145_C146AAAAA00710.20 AA00
1391u6b_B_C146_C147AAAAA00740.18 AA00
1401u6b_B_C147_U148AAAAA00680.31 AA00
1411u6b_B_U148_A149NANNANT00.55 AB04
1421u6b_B_A149_A150OPNOP26280.41 OP26
1431u6b_B_A150_G151AAAAA08670.38 AA08
1441u6b_B_G151_G152AAAAA00570.28 AA00
1451u6b_B_G152_C153AAAAA08780.21 AA08
1461u6b_B_C153_A154AAAAA00630.40 AA00
1471u6b_B_A154_A155OPNOP04640.36 OP04
1481u6b_B_A155_A156AAAAA08510.38 AA08
1491u6b_B_A156_C157AAuAA12650.34 AA12
1501u6b_B_C157_G158NANNANT00.82 AA05
1511u6b_B_G158_C159AAAAA00540.31 AA00
1521u6b_B_C159_U160AAAAA08770.27 AA08
1531u6b_B_U160_A161NANNANT00.42 IC04
1541u6b_B_A161_U162NANNANT01.44 AA11
1551u6b_B_U162_G163NANNANT00.79 OP12
1561u6b_B_G163_G164AAwAA01710.22 AA01
1571u6b_B_G164_U165AAAAA08660.26 AA08
1581u6b_B_U165_G166AAAAA00400.27 AA00
1591u6b_B_G166_A167OPNOP06620.51 OP06
1601u6b_B_A167_A168AAAAA09670.22 AA09
1611u6b_B_A168_G169SYNAB2S540.28 AB2S
1621u6b_B_G169_G170NANNANT01.31 OPS1
1631u6b_B_G170_C171NANNANT00.95 OP21
1641u6b_B_C171_A172NANNANT01.32 OP22
1651u6b_B_A172_U173NANNANT00.51 OP26
1661u6b_B_U173_A174AAAAA08660.31 AA08
1671u6b_B_A174_G175AAwAA01580.32 AA01
1681u6b_B_G175_U176AAAAA08870.18 AA08
1691u6b_B_U176_C177AAAAA00840.35 AA00
1701u6b_B_C177_C178AAAAA08660.32 AA08
1711u6b_B_C178_A179AAwAA06520.28 AA06
1721u6b_B_A179_G180AAAAA00190.53 AA00
1731u6b_B_G180_G181AAAAA00850.10 AA00
1741u6b_B_G181_G182AAAAA00150.46 AA00
1751u6b_B_G182_A183NANNANT01.94 ZZ2S
1761u6b_B_A183_G184NANNANT01.16 OP12
1771u6b_B_G184_U185AAAAA00880.16 AA00
1781u6b_B_U185_G186AAAAA00670.18 AA00
1791u6b_B_G186_G187AAAAA00820.16 AA00
1801u6b_B_G187_C188AAAAA08920.17 AA08
1811u6b_B_C188_G189AAAAA00430.42 AA00
1821u6b_B_G189_A23190NANNANT00.45 OP04
1831u6b_B_C1001_C1002AAAAA00800.20 AA00
1841u6b_B_C1002_A1003AAwAA11710.29 AA11
1851u6b_B_A1003_U1004NANNANT00.48 AA03
1861u6b_B_U1004_U1005ICLIC02540.27 IC02
1871u6b_B_U1005_G1006ZZZZZ02670.62 ZZ02
1881u6b_B_G1006_C1007NANNANT00.69 IC02
1891u6b_B_C1007_A1008NANNANT01.02 AB02
1901u6b_B_A1008_C1009AAwAA01290.35 AA01
1911u6b_B_C1009_U1010NANNANT00.99 OP30
1921u6b_B_U1010_C1011NANNANT00.44 AA12
1931u6b_B_C1011_C1012AAwAA11180.42 AA11
1941u6b_B_C1012_G1013NANNANT01.42 OP17
1951u6b_B_G1013_G1014AAwAA06510.26 AA06
1961u6b_B_G1014_C112AAwAA11570.42 AA11
1971u6b_C_A1_C2AAAAA00930.17 AA00
1981u6b_C_C2_G3AAAAA00590.23 AA00
1991u6b_C_G3_G4NANNANT00.50 AA06
2001u6b_C_G4_C5AAAAA00610.29 AA00
2011u6b_C_C5_C6AAwAA06560.39 AA06
2021u6b_C_A191_A192AAAAA08550.39 AA08
2031u6b_C_A192_G193AAwAA05820.17 AA05
2041u6b_C_G193_C194AAAAA08810.13 AA08
2051u6b_C_C194_C195AAAAA00890.13 AA00
2061u6b_C_C195_A196AAwAA0190.39 AA01
2071u6b_C_A196_C197AAwAA11750.27 AA11
2081u6b_C_C197_A198AAAAA00100.51 AA00
2091u6b_C_A198_C199AAAAA00430.26 AA00
2101u6b_C_C199_A200NANNANT01.15 AA13
2111u6b_C_A200_A201AAAAA00300.40 AA00
2121u6b_C_A201_A202AAwAA06200.37 AA06
2131u6b_C_A202_C203AAAAA08150.71 AA08
2141u6b_C_C203_C204AAAAA00760.19 AA00
2151u6b_C_C204_A205NANNANT00.78 BB2S
2161u6b_C_A205_G206NANNANT01.04 OPS1
2171u6b_C_G206_A1NANNANT01.73 OP06
2181u6b_D_A2_5MU1AAAAA00430.34 AA00
2191u6b_D_C3_A2AAAAA00520.25 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