A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 4-Dec-2019 number of released structures: 10490
Search for released structures

NDB ID: PR0076  PDB ID: 1M5P 


Base Pair Morphology Step Parameters

CSV Format

Model NumberStep NumberStep NameShiftSlideRiseTiltRollTwistX-DisplacementY-DisplacementHelical RiseInclinationTipHelical Twist
14AA_A5C6:G86U87_BB0.168-1.2053.0070.4810.79841.199-1.792-0.1912.9861.134-0.68341.209
18AA_A10C11:G11U12_BB1.316-1.2083.1441.5328.231.33-3.503-2.112.80614.858-2.77632.394
12AA_C3C4:G88G89_BB-1.509-1.2532.7358.47814.74322.178-4.8974.4521.07732.82-18.87427.883
13AA_C4A5:U87G88_BB0.531-1.0283.709-11.44518.51827.576-4.57-2.6512.23733.08820.45135.002
15AA_C6C7:G85G86_BB-0.077-2.3233.619-1.93912.09333.677-5.507-0.1512.65520.0683.21735.774
16AA_C7G9:C13G85_BB0.819-2.4276.272-2.45723.58567.329-3.582-0.8615.25720.6312.14970.916
11AA_G2C3:G89C90_BB1.358-1.0743.3162.145-1.41346.372-1.239-1.5363.401-1.793-2.72146.439
17AA_G9A10:U12C13_BB-1.038-1.6473.3910.3621.20829.765-3.4622.0963.3112.35-0.70429.791
125MB_5CG13A57:A24C25_BB-2.050.4152.717-3.5733.065-28.66-1.358-4.7062.393-6.138-7.156-29.036
110MM_C16U17:A5G6_BB-0.178-0.7393.83-11.10913.12138.048-2.637-1.1013.33618.98816.07741.621
112MM_C18U19:A3G4_BB-0.252-1.8913.5330.76711.75124.231-6.9330.7292.36726.111-1.70526.902
114MM_C20C21:G1G2_BB-0.157-1.7483.532-4.1689.5928.237-5.333-0.5512.79618.8598.19630.074
19MM_U14C16:G6G8_BB-0.07-1.6226.489-6.14615.82879.926-2.032-0.2526.13212.1964.73681.413
111MM_U17C18:G4A5_BB-0.5-1.6093.182-2.241.19437.762-2.6290.4923.1551.8423.45637.844
113MM_U19C20:G2A3_BB0.433-1.3473.1332.2796.44636.994-2.868-0.3972.88710.054-3.55537.599
126BB_A57A59:A23A24_BB3.11-3.3933.5017.5910.43673.393-2.843-2.3243.7450.364-6.33573.731
127BB_A59U60:A22A23_BB-0.037-2.713.5587.9462.66647.352-3.5520.7123.3623.29-9.80448.046
129BB_A62C63:A20G21_BB0.353-1.3923.302-4.4244.34356.519-1.701-0.6143.1634.5714.65656.83
136BB_A69C70:G83U84_BB0.435-1.7022.7222.76612.20922.814-6.184-0.4231.65128.295-6.4125.983
130BB_C63C64:G19A20_BB-0.518-1.1953.708-7.2679.23146.635-2.28-0.0023.46511.4489.01248.012
131BB_C64U65:A18G19_BB0.292-1.8873.136-0.2816.68528.226-5.087-0.6392.62613.4690.56528.992
137BB_C70G71:C82G83_BB1.051-1.6983.711-11.08919.439.638-3.919-2.3442.32326.23914.99845.281
115BB_G46G47:C34C35_BB-0.12-1.8193.5356.1134.53534.528-3.6971.143.217.526-10.14635.332
116BB_G47G48:C33C34_BB-0.283-1.7613.6610.6199.81433.797-4.4480.5663.04116.453-1.03735.159
117BB_G48U49:A32C33_BB-0.224-1.4223.181-4.33912.37928.01-4.816-0.3312.36423.9828.40630.874
120BB_G51G52:C29C30_BB0.454-1.6913.287-3.39310.00328.817-5.002-1.472.50519.36.54730.653
121BB_G52U53:A28C29_BB0.134-1.2483.209-1.4194.13735.716-2.586-0.4123.0436.7142.30335.974
123BB_G54G55:A26C27_BB-0.926-0.5362.5894.3388.78733.013-1.9422.0762.24115.054-7.43334.398
124BM_G555CG13:C25A26_BB-0.741-2.0494.237-6.4043.00738.426-3.5330.1134.1374.5229.6339.047
133BB_G66G67:C16C17_BB1.231-1.572.9561.1379.89520.677-6.78-2.7732.0625.73-2.95622.928
134BB_G67U68:A15C16_BB-0.366-1.7483.492.853-7.4347.636-1.4980.6943.681-9.124-3.50448.258
138BB_G71G72:U81C82_BB-1.11-2.1223.54-0.5395.79930.005-5.2061.9983.10311.0691.02830.552
139BB_G72G73:U80U81_BB0.416-3.506-0.683-172.49128.37135.646-1.727-0.045-1.00214.21686.435178.041
140BB_G73G74:C79U80_BB-0.477-3.046-2.321128.946-91.20551.679-1.933-0.3040.201-49.168-69.513160.17
141BB_G74G75:A78C79_BB-2.931-1.342.3020.297-2.48560.344-1.2462.9242.337-2.471-0.29560.391
118BB_U49U50:A31A32_BB0.458-0.8672.983.2261.08929.505-1.901-0.2732.9792.129-6.30829.696
119BB_U50G51:C30A31_BB0.642-1.1253.4294.26214.59231.987-3.995-0.4332.73624.806-7.24535.33
122BB_U53G54:C27A28_BB-0.018-1.8483.336.19811.41529.669-5.1761.0412.42121.067-11.43832.329
128BB_U60A62:G21A22_BB2.242-0.5523.37-3.6231.6311.509-4.483-14.7572.4487.82717.39912.173
132BB_U65G66:C17A18_BB-0.202-1.9922.8553.9797.53330.263-4.8070.9682.26114.081-7.43831.412
135BB_U68A69:U84A15_BB-0.006-1.0393.0040.59725.66434.77-3.5280.0571.84937.318-0.86842.983
146DD_A5C6:G86U87_EE0.354-0.9743.029-3.83514.18737.441-2.831-0.8982.46921.1325.71240.125
151DD_A10C11:G11U12_EE1.291-1.5383.3322.7546.06626.442-4.76-2.063.02613.0-5.90327.254
153DP_A12U14:G8A9_EE-1.2290.3212.69713.0811.98.3890.26410.8130.4638.298-57.13715.646
144DD_C3C4:G88G89_EE-0.924-1.33.191-3.0913.21425.632-5.2341.2322.34527.4686.42328.949
145DD_C4A5:U87G88_EE-1.226-1.7663.1883.3978.63132.235-4.3252.6232.50715.158-5.96633.509
147DD_C6C7:G85G86_EE0.253-2.8874.077-1.5391.09726.984-6.514-1.0193.9382.3483.29327.049
148DD_C7U8:A14G85_EE0.854-1.4773.1261.90612.22937.973-3.432-1.0552.58618.211-2.83939.868
152DD_C11A12:A9G11_EE0.394-1.2575.013-1.87729.80374.503-2.187-0.3844.33823.7281.49579.451
142DD_G1G2:C90C91_EE-2.182-2.9333.7424.47116.03423.146-8.9775.281.08734.773-9.69728.443
143DD_G2C3:G89C90_EE1.336-0.6862.868-4.8185.83541.658-1.453-2.2662.598.1246.70742.31
150DD_G9A10:U12C13_EE-0.845-1.6533.15-0.3134.60833.826-3.4971.3932.9147.8740.53434.131
149DD_U8G9:C13A14_EE0.52-1.0023.085-3.1167.53231.862-2.934-1.4012.72213.4475.56332.862
171PE_5CG13A57:A24C25_EE-1.851-0.0673.1120.056.748-31.826-1.008-3.2983.064-12.1350.089-32.515
155PP_C15C16:G6A7_EE-0.415-1.2753.786-10.5768.2244.447-2.418-0.4983.51610.58513.61946.323
156PP_C16U17:A5G6_EE0.526-1.7713.5560.18313.31632.048-4.995-0.8562.63822.921-0.31434.638
158PP_C18U19:A3G4_EE-0.726-2.0653.252-4.4713.85425.776-5.5070.4372.9978.4989.85826.432
160PP_C20C21:G1G2_EE-0.015-2.2313.64-10.60411.47532.394-5.278-1.5072.60619.23517.77635.874
154PP_U14C15:A7G8_EE-0.464-0.6753.541-5.30811.82250.287-1.6240.1493.34313.6536.1351.825
157PP_U17C18:G4A5_EE0.342-1.2213.249-2.0560.52531.942-2.307-0.9863.2020.9533.73132.011
159PP_U19C20:G2A3_EE0.11-1.0773.1625.9172.00838.27-1.8590.533.0863.037-8.95238.758
172EE_A57A59:A23A24_EE2.963-3.4893.6567.8613.63671.664-3.102-2.2193.7643.094-6.68972.116
173EE_A59U60:A22A23_EE0.028-2.5183.3339.549-0.77448.718-2.9430.6893.319-0.927-11.44749.595
175EE_A62C63:A20G21_EE0.336-1.0723.223-3.0857.67161.272-1.389-0.4663.0647.493.01261.774
182EE_A69C70:G83U84_EE0.418-0.6663.419-4.5946.34540.152-1.667-1.1153.2169.1366.61540.878
176EE_C63C64:G19A20_EE-0.512-1.1663.538-2.9117.35839.411-2.5810.3963.30510.7784.26440.167
177EE_C64U65:A18G19_EE0.851-1.4993.467-6.2111.73832.557-4.18-2.3072.5919.93410.54735.093
183EE_C70G71:C82G83_EE-1.358-1.3863.3153.6349.7731.43-3.9712.9572.6117.445-6.48933.072
161EE_G46G47:C34C35_EE-0.338-1.9213.3871.8512.86832.64-3.8960.9193.1885.086-3.28332.813
162EE_G47G48:C33C34_EE0.035-1.9273.5230.59411.81431.341-5.2520.0342.64420.958-1.05433.447
163EE_G48U49:A32C33_EE-0.672-1.3533.074-1.47212.22632.52-3.9040.9292.44920.922.51834.715
166EE_G51G52:C29C30_EE0.546-1.4913.2852.8188.21429.681-4.316-0.5042.81915.619-5.35830.898
167EE_G52U53:A28C29_EE0.552-0.9333.0030.6345.25932.722-2.431-0.8722.8329.258-1.11633.136
169EE_G54G55:A26C27_EE-1.362-0.5792.615.6468.1433.818-1.8622.8792.16913.633-9.45735.199
170EP_G555CG13:C25A26_EE-0.275-2.3593.636-10.6311.66741.602-3.408-0.7973.5082.30114.67542.912
179EE_G66G67:C16C17_EE0.259-1.6833.243-1.410.05728.023-5.176-0.7682.48719.9582.77829.771
180EE_G67U68:A15C16_EE-0.009-2.2833.191-2.6955.61339.346-3.956-0.2772.8468.2743.97339.816
184EE_G71G73:U80C82_EE1.264-3.5246.1963.65219.42251.089-5.888-0.9964.7421.618-4.06454.538
185EE_G73G74:C79U80_EE0.862-1.5353.678-1.7336.45228.861-4.46-2.0773.2112.7313.4229.608
164EE_U49U50:A31A32_EE-0.24-0.9083.085-2.9053.86230.368-2.416-0.0772.9597.3155.50230.742
165EE_U50G51:C30A31_EE0.737-1.5263.4272.3079.09732.126-4.147-0.9012.94216.016-4.06233.434
168EE_U53G54:C27A28_EE0.29-1.5833.5275.89115.65329.566-5.1750.4282.42328.026-10.54833.877
174EE_U60A62:G21A22_EE2.526-0.7863.328-5.2720.1427.534-5.146-24.7831.270.94135.0159.194
178EE_U65G66:C17A18_EE-0.753-1.6972.7773.35110.2127.763-4.9081.9921.94220.339-6.67529.732
181EE_U68A69:U84A15_EE0.436-0.9193.0270.50810.75627.033-3.9-0.7712.49321.936-1.03529.061

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.