A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 27-Oct-2021 number of released structures: 11731
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NDB ID: 5LYB  PDB ID: 5LYB 


Base Pair Morphology Step Parameters

CSV Format

Model NumberStep NumberStep NameShiftSlideRiseTiltRollTwistX-DisplacementY-DisplacementHelical RiseInclinationTipHelical Twist
14022_A39A40:G467C469_221.869-2.3063.499-9.818-4.912-8.68514.946-3.2772.67623.161-46.291-13.99
14122_A40A41:U466G467_22-0.026-0.3463.475-5.4249.51362.589-0.772-0.2283.3889.0825.17963.444
14222_A41A438:G465U466_220.0690.2623.6752.3944.75573.7160.0490.0283.6853.959-1.99373.881
15822_A67G69:U82G83_220.804-0.6693.489-7.7410.73255.601-0.755-1.3183.3510.788.25456.1
16022_A93A399:U395G396_22-2.002-0.0482.73-4.7312.482-3.528-5.779-29.7680.045-26.288-50.108-6.401
17822_A103C309:G357U358_221.119-1.7782.993-13.558-0.25893.262-1.211-0.9872.854-0.1769.28794.016
17722_A105A103:U358C308_224.264-4.934-1.49741.65896.15926.535-1.094-3.505-3.14273.386-31.792107.132
18522_A108G109:C305U306_220.165-0.8813.350.39312.51736.888-2.821-0.2012.91219.117-0.638.886
18922_A112U113:A301U302_22-1.112-1.6612.8445.00310.12420.541-6.563.9591.55426.006-12.85323.412
19822_A124U125:U292U293_220.93-0.8643.208-0.1565.06145.379-1.542-1.2123.0966.5360.20145.646
110022_A138G142:A173A266_225.744-1.7754.309-11.4993.57777.436-1.526-4.9383.4922.8439.1478.221
110422_A145U146:A168A169_22-0.409-1.2043.301-15.964-5.49536.931-1.084-1.3143.335-8.17223.73940.484
110622_A147A148:C166U167_221.102-2.0793.8553.67311.39348.676-3.385-1.0043.38813.585-4.37950.039
110722_A148C149:G165C166_224.037-2.9853.785-6.60923.54243.762-5.037-5.2111.49929.0528.15649.836
111322_A182U183:A202U203_22-0.199-1.1683.3181.55312.9926.279-4.930.7072.46326.577-3.17829.304
111922_A188C189:G196A197_220.497-0.8383.59-2.468-11.07955.822-0.193-0.6753.659-11.6992.60756.873
112422_A206U207:C258U259_220.718-1.5073.60.27719.06633.761-4.607-1.0522.44330.041-0.43638.637
112822_A210U211:A254U255_220.759-1.9513.7613.6346.32929.681-5.089-0.6463.3512.125-6.96230.546
113122_A213G214:A251U252_22-0.89-1.1673.3123.70612.86162.547-1.6490.9992.99512.239-3.52763.821
113322_A218U843:A829U830_220.716-0.424-4.639152.47625.583-103.0570.463-1.12-4.056-13.23778.894-164.282
113722_A220A221:U840U841_220.118-2.5293.634.906-5.69926.943-3.6221.1464.028-11.939-10.27827.954
113822_A221A222:U839U840_22-1.254-2.313.154-0.92117.02328.598-6.2832.0731.60131.2051.68933.202
113922_A222U223:G838U839_220.302-1.6473.199-2.5883.86135.017-3.256-0.8612.9776.3824.27835.314
114222_A225A226:U835U836_22-0.071-1.333.496-3.97921.80325.038-5.702-0.4941.79541.4157.55933.321
114322_A226U227:G834U835_220.631-1.6462.7313.763-0.55646.176-2.052-0.5322.79-0.707-4.78846.324
114822_A265U267:A288U289_22-1.868-0.9942.7643.4691.4946.108-1.372.622.5931.899-4.4246.254
18322_A312A315:A352A353_225.209-0.5062.9813.221-19.8057.6438.292-12.4222.315-68.457-11.13221.458
115622_A316C317:G347U348_22-0.167-2.1243.3342.6873.07230.631-4.5740.8273.0865.782-5.05830.896
115922_A323U324:A344U345_22-0.952-1.0433.149-4.0220.56737.625-3.2850.9382.38229.2815.72342.883
116422_A328G329:C339U340_220.427-1.7292.945-0.646-0.05130.786-3.248-0.9182.938-0.0971.21630.792
116722_A366A367:U374U375_22-0.619-1.4883.1470.3836.28434.956-3.2881.0672.83910.356-0.63235.501
116822_A367U368:G373U374_220.07-1.3213.1420.2654.08541.119-2.286-0.0723.0035.798-0.37741.314
16122_A399A401:C394U395_22-0.411-1.6043.229-7.741-0.3337.453-2.408-0.3493.26-0.50711.89938.218
16222_A401G404:C393C394_223.496-1.2953.7510.748-2.98575.161-0.956-2.8383.822-2.447-0.61375.214
16622_A407C408:G389G390_22-1.3871.1442.954-0.6439.063-18.282-6.546-4.1522.103-26.504-1.88-20.398
16922_A410C411:G422G423_221.077-1.4152.636-4.0216.7122.151-5.1-3.6181.90816.80510.07123.476
14322_A438U439:A464G465_22-3.44-3.1392.87918.6312.96511.733-8.40910.517-1.7679.18-57.67422.188
14522_A441C442:G462U463_22-0.748-2.2773.268-1.1668.04935.628-4.6661.0442.72912.9481.87636.516
15622_A452G63:C87U88_22-3.071-1.6533.01-0.095-0.57557.374-1.6933.1933.03-0.5990.09857.376
1122_A468G595:C31U32_221.647-2.8323.533-5.8565.94178.529-2.397-1.4623.2384.6814.61478.9
117422_A477A478:G510A511_22-0.551-2.6573.633-1.8026.33324.998-7.7360.7222.91314.3174.07325.837
117522_A478C479:G509G510_220.564-1.0652.7531.172-5.95528.9-0.978-0.8892.929-11.768-2.31729.518
117722_A485G486:U501U502_221.63-2.1384.36610.2117.2719.465-8.7470.7253.73119.146-26.89223.119
118022_A515G516:C536G537_221.198-0.6293.604-2.6298.51356.097-1.175-1.4193.4288.9892.77656.743
118122_A518A520:U532U533_22-2.675-1.1613.3478.24626.93149.771-2.5683.2272.08529.451-9.01756.743
118222_A520A521:C531U532_22-1.577-1.5133.6296.62615.72431.172-4.713.5282.26226.887-11.32935.435
118322_A521U522:C530C531_22-0.372-1.4753.626-0.2675.24247.434-2.2780.4373.4556.4930.33147.707
118922_A550G557:C587U588_22-1.855-0.812.844-1.58-0.50540.992-1.1072.4952.92-0.7212.25541.024
119622_A567G568:C575G576_220.593-1.4522.715-0.16314.0746.482-2.609-0.7332.21117.3670.20248.452
1622_A599U600:A26U27_220.993-1.0753.0251.1337.06527.722-3.601-1.782.71114.442-2.31728.613
1822_A601U602:G23U24_220.052-1.1323.0894.966.740.336-2.2770.422.8599.593-7.10141.154
11122_A604C4:G20U21_22-2.79-1.2845.22133.9015.19548.457-1.6755.242.7495.595-36.51358.762
120122_A615G616:C1105U1106_22-0.341-1.9063.5874.7889.44831.606-4.9161.4012.83516.768-8.49733.291
120322_A622G1032:U1103U1104_220.863-3.2373.1479.3488.3284.11-19.7682.594-0.4547.822-53.68413.175
127122_A746C747:G802U805_223.887-1.1234.472-38.0673.82358.46-1.144-4.9411.8483.53635.20968.929
127722_A760G761:A789U790_22-0.617-0.5813.4983.0792.61765.966-0.6450.6983.4472.401-2.82566.076
127922_A774G775:U785C786_220.307-5.0121.963131.517-109.54165.337-1.4751.093.958-56.07-67.319172.561
113522_A844G845:C827U828_22-0.482-1.5423.445-9.1447.59528.541-4.402-0.9062.9614.62917.61330.87
122122_A865G866:C962U965_222.818-1.8333.0511.4825.66547.619-2.664-3.362.9096.986-1.82847.957
122522_A869C870:G957U958_220.271-0.7352.949-0.1138.2644.509-1.606-0.3612.77610.7940.14845.231
123622_A881U882:U946U947_220.707-0.6712.505-6.483-0.92840.903-0.875-1.5222.384-1.3189.20541.402
123922_A884G885:C927U928_22-0.086-0.9943.1044.3023.46331.486-2.390.8832.9436.321-7.85131.955
124222_A887U888:A924G925_220.071-0.7543.412-2.4487.01733.647-2.388-0.5093.18211.9424.16634.434
124622_A891A892:U920U921_22-0.795-1.0493.158-6.1888.11330.382-3.2950.3792.89114.9611.41132.011
124722_A892U893:A919U920_220.772-1.6443.1720.6619.03928.188-4.937-1.3852.55117.981-1.31629.581
128422_A933U935:G876A944_220.056-2.8730.02149.11170.72-176.3771.4360.0280.057-35.36274.559-179.528
120822_A966A967:U632U633_22-1.328-1.8923.042-3.8715.12136.569-3.5971.6152.8818.0856.11137.109
120922_A967U968:G631U632_220.365-1.0283.284.0034.63937.453-2.169-0.0553.1567.166-6.18337.933
121222_A970A971:G628U629_225.398-1.6483.1931.0822.37934.151-3.168-8.9993.2394.043-1.83934.248
121322_A971G972:C627G628_220.595-0.8723.846-0.19611.564.325-1.36-0.5623.65910.7110.18365.236
121522_A973A974:C625U626_22-0.663-1.4592.957-8.9783.29626.469-3.709-0.5582.8276.91718.84228.115
121622_A974C975:G624C625_220.01-1.7313.2580.094-1.13335.582-2.665-0.0023.31-1.853-0.15535.6
128822_A979G980:C1021C1022_220.026-1.5364.2052.58216.56752.403-2.8820.1613.60118.238-2.84254.839
129222_A983G984:U1017U1018_220.276-1.9583.0771.38619.79217.316-7.933-0.3540.58949.16-3.44426.277
129722_A992A993:G1011U1012_22-4.0840.5524.335-119.711-123.692-81.3150.6-2.8930.97662.829-60.807-174.036
129822_A993G994:C1010G1011_220.125-0.5423.591-2.8819.15655.113-1.15-0.3133.4589.8123.08855.878
130022_A995U996:G1008U1009_220.591-1.8693.3192.4985.44733.069-4.105-0.6243.0179.472-4.34433.593
130222_A1036C1037:G1094U1095_221.027-1.5783.1490.3115.21836.222-3.181-1.5972.918.34-0.49736.585
130422_A1061U1063:U1056U1058_226.348-2.691-0.65461.702137.859-63.6281.6643.12-0.468-75.07133.599-155.462
130722_A1065C1066:G1053U1054_221.028-2.3363.269-1.6064.06132.555-4.792-2.082.9117.2042.84932.838
131122_A1069C1070:G1048U1049_220.208-1.7883.251-1.0520.08631.003-3.36-0.5893.2380.1611.96731.021
131822_A1076C1077:G1041G1042_220.959-1.2142.808-0.822-1.71226.944-2.221-2.2342.848-3.6691.76127.009
132822_A1113U1115:A1131A1132_221.4752.9950.749-125.347120.242-33.028-1.4990.74-0.754-61.683-64.301-173.955
133022_A1116U1117:U313G1130_22-4.071-1.8762.8441.42917.63532.401-4.6686.5861.48529.059-2.35536.803
11622_A1138A1139:U8G16_22-2.525-1.6962.9626.9120.03.776-12.35227.746-0.7940.001-61.3897.875
11722_A1139G1140:C14U8_223.527-1.1493.992-11.44515.189.662-1.145-2.7263.44110.6128.04491.223
12022_A1142A1143:A11U12_220.245-1.7293.7617.7015.64338.745-3.2690.6393.478.353-11.39839.86
12122_A1143U1144:G10A11_22-0.704-1.7773.2861.0144.63130.762-4.1651.4982.9698.665-1.89631.116
12522_A1147C1148:G1629U1630_22-0.207-1.3463.395-0.8914.02233.403-4.0710.2132.64123.1631.47136.16
12822_A1151A1152:U1626U1627_22-1.426-1.53.723-1.9973.08236.665-2.8471.9493.6594.8843.16536.842
12922_A1152G1153:C1625U1626_220.148-1.483.022-3.8584.7827.361-4.052-1.1112.6849.9468.02928.029
13422_A1157A1160:U1617U1621_224.863-0.274.261-13.019-13.376110.3820.035-3.1363.876-8.1117.895111.433
13522_A1160C1161:G1616U1617_220.189-1.0763.4772.226-3.91835.907-1.1350.0353.576-6.324-3.59236.179
135722_A1203U1560:U1551G1553_221.1010.136-5.363-19.5140.368-55.896-0.1082.724-4.774-0.38-20.148-58.945
137122_A1211G1212:C1451U1452_220.703-1.9143.749.49717.35726.15-6.4590.4242.20933.01-18.06232.687
137622_A1219C1220:G1263G1264_220.397-0.9533.388-0.1360.66363.104-0.941-0.3863.3780.6340.1363.107
137822_A1221C1222:G1261U1262_220.507-0.9263.143-0.3464.35128.479-2.775-1.0922.9658.7790.69928.805
138022_A1223A1224:U1259U1260_22-0.003-1.5923.62212.81516.64735.745-4.0771.4052.53224.674-18.99441.287
138122_A1230U1231:U1254U1257_226.2610.4312.70410.33812.70254.667-0.258-5.9943.74613.496-10.98356.886
138522_A1234G1245:U1250U1251_222.7151.923-0.454137.401-93.73316.7071.121-1.1421.08-50.157-73.523166.474
138722_A1236G1237:C1248U1249_221.091-1.0293.605-0.8893.7934.256-2.374-1.993.4466.4091.50334.47
138922_A1238U1239:C1246U1247_222.011-1.9932.71510.9839.77896.021-1.471-1.1892.7176.549-7.35696.866
139622_A1275U1276:A1436U1437_220.713-1.6553.137-2.5291.5137.391-2.761-1.4213.0172.3513.93837.502
141122_A1296G1297:A1300U1301_22-4.154-1.9733.1970.36715.9458.657-2.6554.1322.60915.951-0.36860.599
141922_A1336A1410:G1387U1415_225.2563.7343.673120.276-39.633-8.745-2.063.025-3.49727.4883.395-126.805
142322_A1344A1345:U1380U1381_22-0.43-1.2913.1957.1420.25931.442-2.3711.9983.0160.47-12.97132.224
142422_A1345A1348:U1377U1380_221.5511.524.98422.54310.525105.0190.724-0.4915.2516.573-14.078107.069
142522_A1348G1349:C1376U1377_220.019-1.1723.017-10.92615.47823.393-4.892-1.8931.75932.23522.75530.02
143422_A1357G1358:C1365U1366_22-0.367-1.6072.9981.16416.87132.64-4.4150.7121.94827.814-1.9236.654
143622_A1388C1389:G1412G1409_22-2.9995.286-3.082-8.418-3.68535.467.9535.842-2.838-5.92813.54236.594
143822_A1391U1392:A1406U1407_22-0.413-1.813.3272.2077.81536.426-3.8220.9262.86212.314-3.47737.291
142022_A1410C1338:G1386G1387_22-2.777-1.747-0.163119.402-124.583-171.1640.87-1.392-0.11262.359.709-179.427
135422_A1469C1470:G1574G1170_22-0.2870.343.1153.468-3.40823.3031.8751.7652.961-8.322-8.46723.798
144322_A1471C1472:G1536U1538_221.652-3.0243.232-7.14610.591-72.9682.1571.1323.707-8.839-5.965-73.925
144522_A1475C1476:G1531U1532_220.77-1.1092.9693.9334.48938.55-2.151-0.7262.8896.749-5.91438.991
144922_A1479G1480:C1527U1528_22-0.419-2.1263.8793.57515.48833.268-5.5771.1732.61125.332-5.84836.773
145122_A1487G1488:C1518U1519_220.244-1.2822.556-15.434-8.00126.645-1.138-2.7752.356-15.44629.79631.729
136722_A1569A1570:G1541G1542_22-0.095-0.0472.876-2.7729.26729.955-1.613-0.2812.73817.3675.19531.444
136822_A1570C1571:G1540G1541_220.541-0.7883.288-4.7669.90465.014-1.122-0.6893.1119.1464.40265.836
133622_A1576A1577:U1168G1169_221.526-1.4053.886-0.52511.69459.139-2.063-1.5523.56511.7230.52760.183
133722_A1577U1578:G1167U1168_220.084-1.212.8586.9521.24846.813-1.5960.3872.8111.56-8.69247.313
146122_A1586A1587:U1609G1610_22-0.409-0.5762.977-4.944-1.62760.416-0.4980.1863.012-1.6144.90360.619
146222_A1587G1588:U1608U1609_220.026-1.7483.484-1.06910.4533.759-4.41-0.22.83317.4761.78735.31
146722_A1592A1593:U1603U1604_220.461-1.1523.476-1.9014.13344.502-1.908-0.7883.345.442.50244.723
146822_A1593G1594:C1602U1603_22-0.79-1.7152.8474.8291.13828.92-3.5932.4352.6152.258-9.58129.334
151922_A1689G1690:C1711A1712_22-0.44-1.8553.603-7.5715.135-37.7650.675-1.6043.887-22.079-11.043-41.257
147122_A1719G1720:A1681U1682_220.353-0.9812.7928.67923.781103.862-0.885-0.1222.61614.957-5.458106.028
147322_A1721A1722:G1679G1680_22-0.76-0.3982.931-1.2398.43427.946-2.4121.2692.72716.9722.49329.192
147422_A1722U1723:A1678G1679_221.666-1.0613.554-3.037.00262.032-1.361-1.7533.3526.7672.92862.453
148022_A1728C1729:G1672G1673_220.985-1.1013.315-8.6228.01833.151-2.953-2.8452.65513.53214.55235.125
148222_A1730A1731:G1670A1671_220.652-2.0993.2778.3960.107-25.764.4573.4642.931-0.23218.225-27.072
148322_A1731A1732:U1669G1670_220.224-0.8633.733-3.86911.63760.617-1.448-0.423.51211.4043.79161.729
148422_A1732C1733:G1668U1669_22-0.645-1.2693.056-3.221.74937.967-2.1480.6073.0392.684.93538.136
149222_A1740U1741:A1660U1661_220.663-1.4572.9836.6463.87527.632-3.7360.0212.8367.92-13.58428.663
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1335277_U62A63:U16A17_77-0.187-0.9513.0710.09521.8730.24-3.9890.3041.96736.527-0.15837.17
1335977_U70G71:C107A108_770.05-1.6763.2225.0122.40334.866-3.1090.6363.0813.98-8.29935.293
1336577_U78A79:G101A102_775.529-1.5393.379-1.991-2.123-13.7938.50420.4363.8538.714-8.171-14.095
1336877_U81G82:C98G99_77-2.082-2.6673.057-7.2849.26415.353-11.893.0941.94129.62723.29619.333
1337077_U83A84:U96A97_770.08-1.7273.7327.41721.98541.047-4.0440.5322.52528.759-9.70246.904
1227088_A33C32:G331G330_550.5441.959-3.607-6.241-18.01-31.663-5.4061.659-2.09229.867-10.35-36.831
1338488_A40A41:G103A105_88-0.318-0.2162.95-0.584-5.651120.666-0.0760.1782.956-3.2510.336120.747
1338588_A41G42:U102G103_880.743-0.5773.763-7.9719.98556.387-1.201-1.2523.49810.4198.31757.7
1338788_A43A44:U100U101_88-0.396-1.9953.7997.6074.07939.971-3.3611.5053.4585.884-10.97340.855
1338888_A44C45:G58U100_880.416-1.122.942-3.6863.0837.562-2.075-1.0572.7934.765.69637.857
1339588_A65A66:U93C94_88-0.674-0.6083.432-0.0622.06149.049-0.8940.8063.4062.4810.07549.09
1339688_A66U67:A92U93_88-0.37-1.5563.675-10.8796.037.868-3.057-0.8533.3768.95616.23739.783
1227588_C28U27:A336G335_551.0112.241-3.422.124-4.837-24.521-6.5831.706-3.00411.2224.928-25.075
1227388_C30U29:A334G333_550.5142.19-3.4171.313-7.337-25.849-6.5160.783-2.72515.9832.859-26.885
1227188_C32G31:C332G331_550.0521.753-3.1240.054-6.45-33.282-3.9470.081-2.74611.1320.094-33.884
1338988_C45G46:C57G58_881.299-1.6043.1920.9414.99129.648-4.055-2.3212.9289.664-1.82330.071
1339188_C47C62:U55G56_88-0.773-2.3013.35916.61112.948.202-3.3871.8782.34714.993-19.30752.338
1340288_C115G116:C137G107_88-1.819-3.5093.347-0.437-1.6784.198-25.11817.9724.564-21.735.6554.542
1340488_C117C118:G135G136_88-1.264-2.2043.0310.1474.82928.696-5.3092.5442.6269.657-0.29429.092
1340588_C118C119:G134G135_88-0.565-2.353.195-1.5649.33427.986-6.3390.822.33418.6383.12429.513
1340688_C119C120:G133G134_880.127-2.0743.2380.7555.32632.47-4.517-0.1032.8739.443-1.33932.901
1340788_C120U121:G132G133_880.006-2.0893.190.9310.86537.706-4.2710.092.51516.397-1.40439.196
1227288_G31C30:G333C332_550.0811.817-3.4661.315-12.933-31.229-5.131-0.065-2.53722.8252.321-33.765
1338688_G42A43:U101U102_88-0.39-2.5672.925-10.1493.76731.45-5.04-0.7972.6066.70518.06533.216
1339088_G46C47:G56C57_88-0.538-1.5373.281-4.2160.39939.828-2.2910.2993.3040.5836.16740.043
1339288_G49C50:G75C76_880.557-1.2323.017-0.5873.19631.767-2.763-1.1092.8725.821.0731.929
1339388_G63U64:A96A97_88-0.411-2.6623.571-6.9865.47728.75-6.293-0.6883.03810.71213.66330.061
1339888_G68U69:A89C91_880.702-1.4183.014.0934.95827.593-3.929-0.5842.7910.219-8.43728.318
1340088_G70A71:G87A88_88-0.075-1.8544.811-0.213-6.432-6.26730.25-1.0922.03145.779-1.518-8.981
1340188_G114C115:G107C108_88-0.09-2.213.201-1.4131.90739.896-3.444-0.0253.0972.7912.06939.964
1340388_G116C117:G136C137_880.76-1.6573.263-2.6775.04740.173-2.93-1.3822.9877.3033.87340.561
1341088_G123G124:C129C130_88-0.044-1.8323.6098.34913.24936.196-4.3151.0692.72620.202-12.7339.334
1227785_U26C339:G25G337_850.3043.0140.731-147.28279.607-19.228-1.4560.263-1.026-42.293-78.247-167.597
1227688_U27U26:G337A336_55-0.3371.427-2.526-3.301-4.788-30.761-3.32-0.16-2.3068.926-6.154-31.293
1227488_U29C28:G335A334_55-0.521.693-2.882-2.083-1.999-32.647-3.301-0.61-2.8033.547-3.697-32.771
1339488_U64A65:C94A96_884.114-2.0413.057-17.1667.75234.619-3.585-7.3340.57311.99226.55639.273
1339788_U67G68:C91A92_88-0.337-1.5073.0964.0681.16342.347-2.1870.853.0121.605-5.61542.549
1339988_U69G70:A88A89_880.2941.2932.844-1.55614.78459.9830.629-0.3543.0514.5461.53161.631
1340888_U121U122:A131G132_880.167-2.4182.8720.5159.11322.084-8.033-0.2791.75122.589-1.27623.874
1340988_U122G123:C130A131_88-0.437-1.9542.651-0.2042.79325.694-4.9750.9332.4326.2570.45825.844

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.