A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 22-Jun-2022 number of released structures: 12128
Search for released structures

NDB ID: 5DNM  PDB ID: 5DNM 


Base Pair Morphology Parameters

CSV Format

Model NumberPair NumberPair NameShearStretchStaggerBucklePropellorOpening
11I_DA-72:DT72_J-1.282-0.1160.141-10.088-10.724-8.073
14I_DA-69:DT69_J0.272-0.115-0.3457.372-7.5055.325
15I_DA-68:DT68_J0.591-0.0410.20911.193-19.332-0.284
17I_DA-66:DT66_J0.816-0.0430.5258.863-17.785-4.053
111I_DA-62:DT62_J0.702-0.3630.9849.085-12.494-9.985
117I_DA-56:DT56_J0.473-0.1390.74119.456-9.8120.762
119I_DA-54:DT54_J0.552-0.027-0.3672.438-8.594-3.402
121I_DA-52:DT52_J0.8630.057-0.585-20.501-15.796-13.9
124I_DA-49:DT49_J-0.476-0.0060.723-6.541-0.9623.349
127I_DA-46:DT46_J0.2280.0230.79432.59-25.849-6.386
128I_DA-45:DT45_J0.937-0.0450.44223.253-33.254-7.812
129I_DA-44:DT44_J0.103-0.3371.0349.449-32.215-2.285
130I_DA-43:DT43_J-0.1790.0130.5679.432-16.575-2.66
135I_DA-38:DT38_J-0.63-0.2770.154-18.678-14.805-12.095
140I_DA-32:DT32_J-1.233-0.151-0.6-3.188-23.8778.926
141I_DA-31:DT31_J-0.8980.0290.1931.804-13.2921.407
142I_DA-30:DT30_J-0.623-0.0090.791-0.172.4732.88
150I_DA-22:DT22_J-0.009-0.0710.87416.0072.823-4.679
153I_DA-19:DT19_J-0.59-0.212-0.171.901-22.705-2.223
154I_DA-18:DT18_J0.3510.090.035-2.192-19.5068.69
155I_DA-17:DT17_J0.4670.0660.201-7.882-16.876-2.735
156I_DA-16:DT16_J-0.084-0.2530.754-0.704-11.209-5.773
159I_DA-12:DT12_J-0.488-0.3020.767-1.41-2.105-9.788
165I_DA-6:DT6_J0.6-0.203-0.471-2.459-26.623-7.07
170I_DA-1:DT1_J-0.4210.031-0.109-0.071-16.032.489
171I_DA0:DT0_J0.569-0.1810.288-4.282-10.7661.177
174I_DA3:DT-3_J-0.4410.0910.1565.879-20.797-2.927
179I_DA8:DT-8_J0.08-0.1770.06-0.474-9.5233.002
180I_DA9:DT-9_J-0.156-0.137-0.0713.094-15.7184.861
182I_DA11:DT-11_J0.113-0.183-0.182-1.041-14.9740.57
192I_DA25:DT-25_J1.469-0.0020.731.958-22.496-15.332
195I_DA28:DT-28_J-1.0060.055-0.52-21.928-17.2270.651
1102I_DA35:DT-35_J-0.4780.1180.4241.581-17.769-3.447
1103I_DA36:DT-36_J0.049-0.1880.6699.544-11.698-4.22
1104I_DA37:DT-37_J0.567-0.2360.35412.547-3.714-2.58
1106I_DA39:DT-39_J-0.089-0.324-0.921-18.808-6.933-1.805
1108I_DA41:DT-41_J0.342-0.348-0.743-11.419-14.263-10.973
1116I_DA50:DC-51_J-1.493-0.216-0.46614.257-28.157-4.622
1123I_DA59:DT-59_J0.5140.4611.09822.577-14.4295.441
1129I_DA65:DT-65_J-0.895-0.13-0.0120.392-13.828-6.3
1131I_DA67:DT-67_J-0.176-0.2510.212-4.062-6.4280.993
1135I_DA71:DT-71_J1.014-0.217-0.2729.31-5.554-3.539
13I_DC-70:DG70_J-0.4960.409-0.045-4.4912.2855.763
19I_DC-64:DG64_J0.305-0.111-0.01210.858-14.97-0.216
110I_DC-63:DG63_J-0.7280.327-0.092.021-21.411.111
112I_DC-61:DG61_J0.3620.666-0.13818.003-19.78514.551
113I_DC-60:DG60_J0.5230.141-0.3810.058-12.61611.951
116I_DC-57:DG57_J0.0760.2820.13511.776-7.2533.647
122I_DC-51:DG51_J1.922-0.2830.09113.022-21.8643.04
125I_DC-48:DG48_J0.650.1150.42314.991-3.5360.526
126I_DC-47:DG47_J0.4120.631-0.88842.229-22.8758.002
143I_DC-29:DG29_J-1.6150.4580.6193.192-7.9964.867
146I_DC-26:DG26_J0.759-0.464-0.8079.245-12.510.865
148I_DC-24:DG24_J0.4-0.1610.024-7.29-2.0320.69
149I_DC-23:DG23_J0.1370.040.057-2.102-10.636-3.138
152I_DC-20:DG20_J-0.609-0.088-0.80628.831-18.2694.257
158I_DC-13:DG13_J1.686-0.2961.273-6.911-16.974-12.881
164I_DC-7:DG7_J0.8930.068-0.46319.809-11.4271.445
167I_DC-4:DG4_J-0.469-0.1870.821-4.902-15.767-0.912
173I_DC2:DG-2_J1.0150.0590.034-2.352-9.0882.669
176I_DC5:DG-5_J0.901-0.430.04.195-6.277-1.377
181I_DC10:DG-10_J0.174-0.026-0.51616.222-6.283-1.303
185I_DC14:DG-14_J0.831-0.275-0.092-0.00110.5680.029
186I_DC15:DG-15_J-1.1070.2880.0225.7390.8635.696
194I_DC27:DG-27_J-0.1750.510.1318.967-27.31314.199
1100I_DC33:DG-33_J0.220.0350.441-8.469-1.176-0.362
1101I_DC34:DG-34_J0.068-0.6041.3711.162-5.848-10.352
1107I_DC40:DG-40_J-0.5540.409-0.10.027-10.2160.958
1109I_DC42:DG-42_J0.245-0.0290.981-24.567-12.2531.415
1119I_DC55:DG-55_J0.08-0.2010.94-23.31-1.823-2.107
1122I_DC58:DG-58_J0.418-0.0690.417-1.976-1.436-1.556
115I_DG-58:DC58_J-0.9760.1810.09-0.278-2.0333.157
118I_DG-55:DC55_J0.0170.2050.46118.981-9.637-1.297
131I_DG-42:DC42_J0.9310.4670.085-5.516-6.3344.179
133I_DG-40:DC40_J-0.953-0.201-0.84-23.776-7.512-7.56
139I_DG-33:DC34_J-0.4032.3740.517-46.779-27.55538.457
145I_DG-27:DC27_J0.128-0.172-0.001-12.8-22.3331.843
157I_DG-15:DC15_J-0.7110.160.4811.1586.3468.35
161I_DG-10:DC10_J-0.914-0.383-0.645-2.77-15.372-1.735
166I_DG-5:DC5_J-0.148-0.014-0.108-4.209-20.840.295
169I_DG-2:DC2_J-0.2440.0940.4927.12-2.8719.791
175I_DG4:DC-4_J0.121-0.170.125.396-24.544-6.38
178I_DG7:DC-7_J-0.232-0.069-0.655-12.251-5.199-1.768
184I_DG13:DC-13_J-0.4780.0530.1597.5326.8551.446
190I_DG23:DC-23_J0.7170.494-0.639-30.35118.192-5.004
191I_DG24:DC-24_J0.589-0.113-0.737-13.43822.5613.299
193I_DG26:DC-26_J0.09-0.231.02215.394-0.275-0.776
196I_DG29:DC-29_J0.5620.750.287-7.506-13.01116.646
1114I_DG47:DC-47_J1.2831.3040.43-19.624-17.59714.747
1115I_DG48:DC-48_J-0.9090.8810.663-5.446-8.13616.544
1117I_DG51:DA-52_J-0.3311.399-1.056-3.217-20.963-2.271
1121I_DG57:DC-57_J-0.228-0.12-0.403-23.127-12.553-1.293
1124I_DG60:DC-60_J0.5140.0610.5323.497-7.922-0.306
1125I_DG61:DC-61_J0.691-0.069-0.1661.698-14.1550.347
1127I_DG63:DC-63_J-0.585-0.208-0.5710.879-3.3270.721
1128I_DG64:DC-64_J-0.444-0.0130.46518.408-5.9817.471
1134I_DG70:DC-70_J-0.536-0.292-0.2940.007-8.942-0.445
12I_DT-71:DA71_J-0.872-0.0740.367-7.051-6.744-2.424
16I_DT-67:DA67_J0.332-0.0270.19910.421-10.613.735
18I_DT-65:DA65_J1.09-0.29-0.3976.033-12.436-8.5
114I_DT-59:DA59_J0.0840.247-0.6775.17-23.62511.5
120I_DT-53:DA53_J0.7110.215-0.85411.096-14.907-24.095
123I_DT-50:DA50_J0.745-0.018-0.0469.158-33.0263.187
132I_DT-41:DA41_J-0.028-0.09-0.383-7.561-9.2270.884
134I_DT-39:DA39_J0.213-0.173-0.129-1.9010.808-4.802
136I_DT-37:DA37_J0.352-0.0360.315-10.2980.453-0.973
137I_DT-36:DA36_J-0.447-0.2780.027-5.153-10.044-5.23
138I_DT-35:DA35_J0.282-0.3671.242-12.378-1.2393.44
144I_DT-28:DA28_J-0.315-0.1980.3035.044-10.2922.384
147I_DT-25:DA25_J-0.282-0.0660.180.349-30.7781.773
151I_DT-21:DA21_J-0.421-0.125-0.15121.602-2.3880.43
160I_DT-11:DA11_J1.271-0.1030.40631.8217.649-3.512
162I_DT-9:DA9_J-0.644-0.090.523-9.067-20.979-0.306
163I_DT-8:DA8_J0.15-0.085-0.0962.259-12.4055.384
168I_DT-3:DA3_J-0.1120.2050.028-6.458-15.476-6.146
172I_DT1:DA-1_J-0.02-0.0970.026-7.868-13.9640.919
177I_DT6:DA-6_J-0.323-0.114-0.0537.662-33.902-4.903
183I_DT12:DA-12_J0.549-0.272-0.6020.792-19.775.739
187I_DT16:DA-16_J-0.2070.290.25610.87210.2971.696
188I_DT18:DA-18_J-0.8890.068-0.6710.903-19.7837.07
189I_DT19:DA-19_J-0.3070.39-1.1219.1129.751-14.52
197I_DT30:DA-30_J0.070.271-0.125-5.213-18.2763.2
198I_DT31:DA-31_J1.0170.1660.549-13.1181.7240.592
199I_DT32:DA-32_J-0.0790.115-0.132-9.791-17.056-19.384
1105I_DT38:DA-38_J-1.5290.16-0.7190.437-8.1129.689
1110I_DT43:DA-43_J0.120.4250.155-19.111-17.1050.104
1111I_DT44:DA-44_J-0.576-0.0321.065-20.624-5.819-6.705
1112I_DT45:DA-45_J-0.419-0.0241.299-20.469-5.6510.794
1113I_DT46:DA-46_J-0.240.51.016-14.396-35.3327.621
1118I_DT54:DA-54_J-0.161-0.139-0.43410.3-29.3565.454
1120I_DT56:DA-56_J-0.203-0.2920.744-15.836-14.0010.973
1126I_DT62:DA-62_J0.412-0.374-0.9599.144-15.6336.292
1130I_DT66:DA-66_J0.3710.0330.03411.717-9.454-1.978
1132I_DT68:DA-68_J-0.158-0.155-0.0573.111-13.3092.396
1133I_DT69:DA-69_J0.047-0.2090.066-3.268-8.794-2.625
1136I_DT72:DA-72_J-0.015-0.397-0.75218.874-4.249-1.24

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.