A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 14-Aug-2019 number of released structures: 10334
Search for released structures

NDB ID: 4YM5  PDB ID: 4YM5 


Base Pair Morphology Step Parameters

CSV Format

Model NumberStep NumberStep NameShiftSlideRiseTiltRollTwistX-DisplacementY-DisplacementHelical RiseInclinationTipHelical Twist
11II_DA1DT2:DA143DT144_JJ0.008-0.7223.0869.15-6.24231.265-0.2491.4773.052-11.152-16.34833.123
14II_DA4DA5:DT140DT141_JJ0.3320.1773.145-5.171-2.33735.0090.618-1.2683.049-3.8548.52635.452
15II_DA5DT6:DA139DT140_JJ-0.284-0.1673.523-5.393-9.44836.9211.03-0.3013.467-14.5358.29838.436
17II_DA7DT8:DA137DT138_JJ-0.063-0.0723.115-2.059-3.08336.590.286-0.1683.11-4.8953.26936.771
111II_DA11DC12:DG133DT134_JJ0.665-0.072.915.416-3.90929.6950.579-0.2822.967-7.507-10.40330.421
117II_DA17DG18:DC127DT128_JJ0.1413.0963.6430.884-3.04444.4774.384-0.0973.436-4.016-1.16744.584
119II_DA19DT20:DA125DT126_JJ0.5210.6183.031.2533.65935.340.512-0.6813.0926.006-2.05635.544
124II_DA24DC25:DG120DT121_JJ0.323-0.1973.126.53-3.88733.7360.250.4323.129-6.594-11.07834.557
127II_DA27DA28:DT117DT118_JJ0.081.7172.88-6.956-12.18737.4933.639-0.7592.191-18.19810.38739.945
132II_DA34DT35:DA109DT110_JJ-0.17-0.5873.417-4.403-4.88926.4240.058-0.8153.45-10.499.44727.217
138II_DA40DA41:DT103DT104_JJ-0.2370.0743.135-1.0146.41929.102-1.1440.2573.08612.5761.98629.804
139II_DA41DA42:DT102DT103_JJ-0.198-0.6283.074-6.9726.72432.74-2.062-0.692.87311.61512.04434.106
140II_DA42DC43:DG101DT102_JJ0.755-0.5373.3725.8441.10330.998-1.203-0.2493.4332.04-10.8131.549
148II_DA50DT51:DA93DT94_JJ-0.4070.8052.640.615.20221.3340.4361.2642.74313.786-1.61721.96
151II_DA53DA54:DT90DT91_JJ-0.493-0.0082.743-2.08510.68122.644-2.690.6142.51625.4024.95925.093
152II_DA54DA55:DT89DT90_JJ-0.0510.3313.3851.7857.3940.191-0.3730.2783.38610.638-2.5740.875
153II_DA55DA56:DT88DT89_JJ1.0071.0572.6715.205-11.20131.7543.218-1.0662.309-19.571-9.09534.014
154II_DA56DG57:DC87DT88_JJ1.1421.8583.643.096-12.60545.0473.445-1.1673.109-16.062-3.94646.786
158II_DA60DT61:DA83DT84_JJ-0.439-0.2572.868-6.0250.37831.211-0.53-0.182.8960.69411.06931.776
164II_DA66DG67:DC77DT78_JJ0.2171.9413.252-2.161-15.67236.634.452-0.5392.253-23.6293.25839.793
169II_DA71DA72:DT72DT73_JJ0.073-0.2943.603-2.41312.08228.03-3.159-0.6583.1923.5564.70430.569
170II_DA72DC73:DG71DT72_JJ-0.036-0.2823.1461.6626.87227.662-2.0630.4352.98414.084-3.40728.535
173II_DA75DG76:DC68DT69_JJ0.0360.283.244-6.522-4.31639.0760.905-0.7993.151-6.3769.63339.821
178II_DA80DA81:DT63DT64_JJ-0.4580.0733.5971.1368.26737.733-1.0110.8473.5212.594-1.73138.612
179II_DA81DC82:DG62DT63_JJ0.203-0.112.75616.972-0.36224.512-0.152.6912.395-0.748-35.09929.742
181II_DA83DG85:DC59DT61_JJ-0.2650.2587.30310.06616.46969.118-1.0431.07.11514.238-8.70371.438
190II_DA93DT94:DA50DT51_JJ0.1010.782.4792.64310.34526.917-0.2840.2682.59421.195-5.41428.921
194II_DA97DG98:DC46DT47_JJ-0.9451.1533.509-2.791-14.33632.5764.0041.1322.838-24.1034.69235.619
197II_DA100DG101:DC43DT44_JJ0.6110.3343.9121.5245.37937.634-0.313-0.7043.9428.282-2.34738.032
1104II_DA107DA108:DT36DT37_JJ0.4912.3773.609-3.125-16.51947.7013.956-0.7972.664-19.7263.73250.413
1105II_DA108DA109:DT35DT36_JJ0.219-0.0733.235-5.848-1.82634.2490.152-1.2453.155-3.079.83234.776
1106II_DA109DT110:DA34DT35_JJ0.252-0.4883.1364.774-3.10530.072-0.3260.4413.171-5.918-9.09830.594
1108II_DA111DC112:DG32DT33_JJ-0.19-0.3273.3062.0862.46635.358-0.8990.6183.264.05-3.42635.5
1110II_DA113DC114:DG30DT31_JJ-0.2730.3363.2478.264-3.21137.5360.8991.4173.083-4.906-12.62838.532
1116II_DA122DG123:DC22DT23_JJ0.366-0.6083.362-3.4912.94333.227-2.843-1.0952.88221.5745.81735.759
1118II_DA124DA125:DT20DT21_JJ-0.010.2673.27-1.3317.46330.885-0.894-0.2293.24113.7552.45331.78
1119II_DA125DT126:DA19DT20_JJ-0.6070.5243.167-4.164.87337.3850.1890.4083.2547.5356.43237.911
1125II_DA131DG132:DC13DT14_JJ0.3361.4623.369-1.68112.43143.360.689-0.6043.6216.4192.2245.054
1131II_DA137DT138:DA7DT8_JJ-0.42-0.4372.812-3.9735.21727.411-1.9430.0672.71610.8158.23628.17
1133II_DA139DT140:DA5DT6_JJ-0.080.142.742.622-9.86240.611.0570.3412.627-13.945-3.70841.82
1137II_DA143DT144:DA1DT2_JJ-0.106-0.6483.575-8.114-13.72844.1870.472-0.6273.58-17.58310.39346.841
13II_DC3DA4:DT141DG142_JJ-0.7460.5993.21911.2861.36931.3770.8283.0882.8132.433-20.06233.325
19II_DC9DC10:DG135DG136_JJ-0.20.232.9489.1672.95138.8670.0321.2382.844.354-13.52439.998
110II_DC10DA11:DT134DG135_JJ-0.483-0.2163.117-2.41814.65525.727-3.350.4612.64629.9434.94129.644
112II_DC12DC13:DG132DG133_JJ0.6190.2773.28511.05515.84636.89-1.3910.3693.19623.194-16.18241.487
113II_DC13DT14:DA131DG132_JJ-0.6060.7463.437-2.34414.6934.714-0.9530.6023.49423.343.72537.676
116II_DC16DA17:DT128DG129_JJ0.541.5653.8884.22711.72637.9350.573-0.1714.20617.471-6.29839.858
122II_DC22DT23:DA122DG123_JJ0.735-0.0173.7053.8559.68437.754-1.357-0.5683.64614.628-5.82339.116
125II_DC25DC26:DG119DG120_JJ0.6320.3433.4364.38411.88135.045-1.174-0.363.42218.981-7.00437.195
126II_DC26DA27:DT118DG119_JJ-0.0593.2333.5061.362-12.01550.944.4380.1552.728-13.748-1.55952.262
141II_DC43DT44:DA100DG101_JJ-0.580.1163.993-3.8694.47442.068-0.3980.3184.0196.1965.35842.463
144II_DC46DT47:DA97DG98_JJ1.5891.1153.1048.02-9.27832.4033.254-1.4812.981-15.931-13.77134.588
146II_DC48DC49:DG95DG96_JJ0.1970.7613.476-0.14715.54639.11-0.734-0.2933.51922.1870.2141.975
147II_DC49DA50:DT94DG95_JJ-0.7450.0293.923-2.52119.06727.656-3.7680.7853.31735.0284.63133.579
150II_DC52DA53:DT91DG92_JJ-0.6311.023.901-2.47313.37733.785-0.7190.5764.0421.9454.05636.347
157II_DC59DA60:DT84DG85_JJ-0.6010.0993.989-3.18810.27244.491-0.9770.4313.94913.3374.13845.709
163II_DC65DA66:DT78DG79_JJ-0.7411.3523.505-2.599.25340.7980.8050.7333.74913.0563.65541.867
166II_DC68DT69:DA75DG76_JJ0.0091.0053.05810.057-1.07442.9151.4340.8722.962-1.444-13.52244.036
171II_DC73DC74:DG70DG71_JJ0.2130.1954.192-13.3525.18635.727-0.531-2.4543.8648.06520.76438.404
172II_DC74DA75:DT69DG70_JJ-1.350.5832.8146.4760.96236.6150.8092.8312.561.516-10.20737.176
175II_DC77DT78:DA66DG67_JJ-1.0581.1253.528-1.37-14.44829.6664.4751.6292.745-26.3262.49732.954
180II_DC82DA83:DT61DG62_JJ0.8080.9123.469-8.11312.00534.968-0.269-2.3823.33319.00212.84137.764
183II_DC86DC87:DG57DG58_JJ-0.5090.7543.272-3.515.86938.6060.4050.3283.3788.7935.25839.185
184II_DC87DT88:DA56DG57_JJ-0.3741.3093.0823.578-7.78133.6393.2621.1182.669-13.181-6.06134.682
196II_DC99DA100:DT44DG45_JJ-1.4250.8423.4472.233-1.28628.6261.9933.3883.289-2.595-4.50428.739
1102II_DC105DC106:DG38DG39_JJ0.9070.73.6185.66-0.50734.6041.247-0.5483.705-0.845-9.43735.054
1103II_DC106DA107:DT37DG38_JJ-0.8570.7363.1683.7386.08631.8560.2792.1593.13410.917-6.70532.627
1109II_DC112DA113:DT31DG32_JJ-0.187-0.763.649-7.49319.20221.664-5.677-1.2762.22841.04216.01529.817
1121II_DC127DT128:DA17DG18_JJ-0.4992.9283.731-2.385-5.39248.7663.970.4043.428-6.5032.87749.1
1124II_DC130DA131:DT14DG15_JJ-0.862.0144.051-4.3946.18636.0552.0920.5824.3969.867.00336.819
115II_DG15DC16:DG129DC130_JJ-1.0910.9442.266-3.0140.4837.4261.4221.4172.3560.7464.68737.546
118II_DG18DA19:DT126DC127_JJ-0.5681.9572.471-5.0220.63334.83.1680.3612.561.0528.34335.155
128II_DG30DT31:DA113DC114_JJ0.470.2512.938-2.676-5.5934.1711.18-1.1512.819-9.4174.50834.712
130II_DG32DT33:DA111DC112_JJ0.02-0.6323.454-0.7411.76634.129-1.369-0.1583.4173.0061.26134.181
136II_DG38DG39:DC105DC106_JJ-0.8770.5153.352-6.831.48536.4680.5990.4173.4722.34710.79137.109
137II_DG39DA40:DT104DC105_JJ0.293-0.1814.1182.28714.05338.877-2.156-0.1063.84220.303-3.30541.307
143II_DG45DC46:DG98DC99_JJ-2.1660.9523.4180.038-10.91242.4862.3272.9073.092-14.768-0.05243.802
155II_DG57DG58:DC86DC87_JJ0.0770.6933.577-0.04811.91636.406-0.634-0.1253.6218.4740.07538.244
156II_DG58DC59:DG85DC86_JJ-0.0690.1313.285-2.756-8.30933.6191.495-0.3073.16-14.0724.66634.708
160II_DG62DT63:DA81DC82_JJ-0.1940.1612.712-3.6785.32432.313-0.476-0.1822.7089.4496.52732.938
165II_DG67DC68:DG76DC77_JJ-0.5110.7033.678-4.196-4.8940.7291.590.2183.607-6.9735.98441.215
168II_DG70DA71:DT73DC74_JJ-1.7940.6253.175-6.5783.85836.2040.4511.9183.4826.12510.44236.972
174II_DG76DC77:DG67DC68_JJ1.1990.1253.4522.611-5.66235.2761.071-1.553.468-9.253-4.26735.805
177II_DG79DA80:DT64DC65_JJ-0.5160.5082.981-8.862-4.57537.491.282-0.2222.944-6.96813.49938.748
182II_DG85DC86:DG58DC59_JJ0.4030.323.011-0.009-8.75835.821.588-0.6382.857-13.9820.01536.841
189II_DG92DA93:DT51DC52_JJ0.5930.0973.4274.3329.03729.725-1.638-0.2273.36317.018-8.15731.333
192II_DG95DG96:DC48DC49_JJ0.0920.4733.130.30114.35936.112-1.023-0.1023.09222.117-0.46438.775
193II_DG96DA97:DT47DC48_JJ0.1650.8162.704-5.417-7.18836.1562.043-0.8352.454-11.3668.56537.223
195II_DG98DC99:DG45DC46_JJ2.5251.0823.7396.731-5.35743.6412.015-2.6033.915-7.123-8.95144.44
198II_DG101DT102:DA42DC43_JJ-0.455-0.792.947-1.7682.25731.27-1.8390.5442.9054.1753.27231.398
1113II_DG119DG120:DC25DC26_JJ-0.1930.3363.3610.3227.62634.382-0.6250.3693.35412.707-0.53735.194
1114II_DG120DT121:DA24DC25_JJ-0.5780.0093.119-3.974-5.00439.410.5680.4063.137-7.3615.84639.904
1117II_DG123DA124:DT21DC22_JJ-0.69-0.1123.7813.6037.5836.155-1.3371.6373.60212.015-5.71237.085
1123II_DG129DC130:DG15DC16_JJ1.1171.6422.5947.5344.20838.7062.003-0.8972.9086.254-11.19839.62
1126II_DG132DG133:DC12DC13_JJ-0.027-0.0353.182-8.6817.98920.52-4.08-1.882.28440.23419.41428.561
1127II_DG133DT134:DA11DC12_JJ-0.7460.52.853-3.2292.0931.8310.5710.8342.9383.7935.86132.057
1129II_DG135DG136:DC9DC10_JJ-0.0970.6042.7030.6233.1138.2610.5950.2132.744.735-0.94938.387
1130II_DG136DA137:DT8DC9_JJ-0.4330.4244.0992.9920.06647.7110.5170.8324.0670.081-3.69547.799
1136II_DG142DA143:DT2DC3_JJ-0.729-0.5273.66-3.3953.86836.514-1.4210.6383.6386.1365.38536.862
12II_DT2DC3:DG142DA143_JJ1.127-0.5713.949-8.0394.43137.315-1.512-2.8813.5516.79912.33638.388
16II_DT6DA7:DT138DA139_JJ0.928-0.1033.67822.8374.04839.116-0.5711.2613.6425.499-31.02545.242
18II_DT8DC9:DG136DA137_JJ1.3730.1313.447-1.4581.436.3910.007-2.4073.3942.2392.33336.445
114II_DT14DG15:DC130DA131_JJ0.781.654.0458.0257.95533.9761.1690.264.37713.17-13.28635.753
120II_DT20DT21:DA124DA125_JJ0.2680.353.251-2.1748.46735.001-0.643-0.7433.22413.8133.54736.043
121II_DT21DC22:DG123DA124_JJ-0.364-0.1013.4951.95812.52335.428-1.8960.8373.25319.813-3.09837.559
123II_DT23DA24:DT121DA122_JJ-0.1350.683.245-5.3133.82430.1680.528-0.7893.2797.24110.05930.854
129II_DT31DG32:DC112DA113_JJ-0.181-0.4964.0292.71617.96227.38-4.5740.8793.133.657-5.08932.762
131II_DT33DA34:DT110DA111_JJ0.4850.1933.4820.5183.29843.559-0.078-0.5983.4934.437-0.69743.68
133II_DT35DT36:DA108DA109_JJ-0.016-0.0353.2737.0621.83932.521-0.3681.2053.1933.233-12.41733.308
134II_DT36DT37:DA107DA108_JJ-0.1152.2882.8834.788-14.83550.1013.3680.382.153-17.049-5.50352.32
135II_DT37DG38:DC106DA107_JJ0.7991.6963.011-3.2251.1132.2212.86-1.9532.9751.9945.7932.396
142II_DT44DG45:DC99DA100_JJ1.3830.5163.266-0.707-1.37831.9471.183-2.6363.211-2.5011.28331.984
145II_DT47DC48:DG96DA97_JJ-0.2440.9352.9045.872-2.41133.8451.9081.2112.753-4.096-9.97834.418
149II_DT51DC52:DG92DA93_JJ0.508-0.3323.141-4.9713.75932.587-2.407-1.5042.68623.1228.35335.639
159II_DT61DG62:DC82DA83_JJ0.414-0.0673.8534.0814.92828.03-1.4470.2523.80610.011-8.2928.737
161II_DT63DT64:DA80DA81_JJ0.6390.2773.0434.2887.72833.322-0.678-0.4433.08413.191-7.31934.442
162II_DT64DC65:DG79DA80_JJ0.5280.5713.1414.3794.81334.7520.242-0.2353.237.971-7.25335.337
167II_DT69DG70:DC74DA75_JJ1.1741.083.688-2.35319.54829.724-1.721-2.3433.60533.8374.07335.531
176II_DT78DG79:DC65DA66_JJ0.9231.5143.736.2270.28649.521.771-0.5693.8210.34-7.449.886
185II_DT88DT89:DA55DA56_JJ-0.9970.7943.044-5.189-14.04138.6482.50.9042.715-20.3127.50741.343
186II_DT89DT90:DA54DA55_JJ0.276-0.0623.941-4.94811.04537.893-1.635-1.0993.71816.5027.39339.711
187II_DT90DT91:DA53DA54_JJ0.3240.6382.91418.38510.64432.544-0.2841.6632.78416.933-29.24738.706
188II_DT91DG92:DC52DA53_JJ0.0481.3123.286-11.78618.95922.124-1.702-2.6573.10138.89824.18131.331
191II_DT94DG95:DC49DA50_JJ0.0430.5554.002-5.10416.70632.316-2.034-0.9593.78527.648.44436.624
199II_DT102DT103:DA41DA42_JJ0.453-0.4093.4973.85311.1137.476-2.019-0.1873.27916.793-5.82439.214
1100II_DT103DT104:DA40DA41_JJ-0.103-0.0643.197-2.3746.58128.52-1.511-0.2963.10313.1114.7329.348
1101II_DT104DC105:DG39DA40_JJ-0.166-0.2613.1132.4356.79236.799-1.2460.563.00310.633-3.81237.476
1107II_DT110DA111:DT33DA34_JJ-0.3260.7453.5220.0622.6144.7850.720.4333.5573.423-0.08144.857
1111II_DT117DT118:DA27DA28_JJ-0.6011.7932.9664.595-8.98344.3482.9951.1222.505-11.72-5.99645.425
1112II_DT118DG119:DC26DA27_JJ-0.4932.653.16-4.345-14.90140.7184.7920.3132.147-20.5365.98843.458
1115II_DT121DA122:DT23DA24_JJ0.0560.7133.322.265.95833.4250.2350.2773.38910.243-3.88534.01
1120II_DT126DC127:DG18DA19_JJ0.8361.3392.9973.067-5.03735.6912.796-0.9592.848-8.149-4.96236.159
1122II_DT128DG129:DC16DA17_JJ-0.2191.4043.347-1.8424.92732.2671.5930.0533.5248.7923.28732.681
1128II_DT134DG135:DC10DA11_JJ0.40.1453.3422.4396.34730.66-0.962-0.2673.32511.821-4.54331.387
1132II_DT138DA139:DT6DA7_JJ-1.151-0.3243.237-10.2352.83437.906-0.830.4543.3924.26115.3939.313
1134II_DT140DT141:DA4DA5_JJ0.6030.5113.3586.609-7.10234.9881.846-0.0153.253-11.541-10.7436.267
1135II_DT141DG142:DC3DA4_JJ0.4740.1953.677-8.85522.13927.283-3.26-2.1952.80338.84315.53736.085

The above values were obtained using first alternate conformation only and calculated by 3DNA program.
Xiang-Jun Lu & Wilma K. Olson (2003). '3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures', Nucleic Acids Res.31(17), 5108-21.
Xiang-Jun Lu & Wilma K. Olson (2008). '3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures', Nat Protoc.3(7), 1213-27.