RNA 3D Hub //

6YDW Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6YDW_0011/AA/8:18No text annotation
geometric
HL_4LFB_001
HL_73535.1
HL_6YDW_0051/AA/147:153No text annotation
geometric
HL_5TBW_018
NA
HL_6YDW_0061/AA/160:165No text annotation
HL_6YDW_0071/AA/198:203No text annotation
geometric
HL_5U3G_001
HL_75660.8
HL_6YDW_0081/AA/248:253GNRA
geometric
HL_1G1X_003
NA
HL_6YDW_0091/AA/342:351No text annotation
geometric
HL_4LFB_015
HL_38491.2
HL_6YDW_0101/AA/376:381No text annotation
geometric
HL_5U3G_001
HL_75660.8
HL_6YDW_0111/AA/426:436No text annotation
geometric
HL_1WZ2_007
HL_75660.8
HL_6YDW_0121/AA/467:477No text annotation
geometric
HL_2Y8W_001
HL_40612.1
HL_6YDW_0131/AA/501:506No text annotation
geometric
HL_2Y9H_003
HL_75660.8
HL_6YDW_0161/AA/636:641Mini UNCG
geometric
HL_5J7L_204
NA
HL_6YDW_0221/AA/941:946No text annotation
geometric
HL_5NFV_001
HL_69752.4
HL_6YDW_0241/AV/28:36tRNA anticodon loop
geometric
HL_4TUE_034
NA
HL_6YDW_0291/BA/54:61No text annotation
geometric
HL_4WF9_006
HL_48677.1
HL_6YDW_0301/BA/80:86No text annotation
geometric
HL_5J7L_141
NA
HL_6YDW_0311/BA/121:126GNRA
geometric
HL_7RQB_063
NA
HL_6YDW_0321/BA/167:175No text annotation
geometric
HL_8C3A_039
NA
HL_6YDW_0331/BA/183:192T-loop with 2 bulged bases not stacked
geometric
HL_4FRN_005
NA
HL_6YDW_0341/BA/220:225No text annotation
geometric
HL_5TBW_006
NA
HL_6YDW_0361/BA/291:300No text annotation
geometric
HL_7RQB_023
NA
HL_6YDW_0371/BA/326:332No text annotation
geometric
HL_4V9F_025
HL_92935.1
HL_6YDW_0381/BA/372:377No text annotation
geometric
HL_7RQB_025
NA
HL_6YDW_0391/BA/401:410No text annotation
HL_6YDW_0401/BA/442:449GNRA
geometric
HL_7A0S_026
HL_34789.4
HL_6YDW_0411/BA/462:469No text annotation
geometric
HL_5NFV_001
HL_69752.4
HL_6YDW_0421/BA/509:519No text annotation
geometric
HL_5J7L_161
NA
HL_6YDW_0441/BA/613:620No text annotation
HL_6YDW_0451/BA/653:658Externally structured
geometric
HL_8C3A_022
NA
HL_6YDW_0461/BA/688:693No text annotation
geometric
HL_2Y8W_001
HL_40612.1
HL_6YDW_0471/BA/731:734Mini UNCG
geometric
HL_5F9R_002
NA
HL_6YDW_0481/BA/760:767No text annotation
geometric
HL_1WZ2_007
HL_75660.8
HL_6YDW_0491/BA/829:839No text annotation
geometric
HL_5TBW_046
NA
HL_6YDW_0501/BA/850:864No text annotation
HL_6YDW_0521/BA/906:915No text annotation
HL_6YDW_0531/BA/944:952No text annotation
geometric
HL_5TBW_050
NA
HL_6YDW_0541/BA/1022:1031No text annotation
geometric
HL_4WF9_047
HL_78372.1
HL_6YDW_0551/BA/1148:1156No text annotation
geometric
HL_7A0S_052
HL_11974.2
HL_6YDW_0561/BA/1164:1176No text annotation
HL_6YDW_0571/BA/1187:1190No text annotation
geometric
HL_5J7L_176
NA
HL_6YDW_0581/BA/1198:1205GNRA with extra cWW
geometric
HL_4WF9_053
HL_87268.2
HL_6YDW_0591/BA/1238:1243No text annotation
HL_6YDW_0601/BA/1294:1302No text annotation
geometric
HL_4V9F_062
HL_52011.1
HL_6YDW_0611/BA/1351:1358GNRA variation
geometric
HL_4WF9_057
HL_46665.2
HL_6YDW_0621/BA/1374:1380No text annotation
geometric
HL_5TBW_063
NA
HL_6YDW_0631/BA/1417:1422GNRA
geometric
HL_7RQB_063
NA
HL_6YDW_0641/BA/1461:1466GNRA
geometric
HL_4Y1M_004
HL_34789.4
HL_6YDW_0651/BA/1489:1495No text annotation
HL_6YDW_0661/BA/1514:1532No text annotation
geometric
HL_7A0S_074
NA
HL_6YDW_0671/BA/1557:1565No text annotation
geometric
HL_7RQB_068
NA
HL_6YDW_0691/BB/32:40tRNA anticodon loop
homologous
HL_6UFM_002
HL_81376.3

Problematic loops

#loop idProblemSequence
HL_6YDW_002No text annotation
HL_6YDW_003No text annotation
HL_6YDW_004No text annotation
HL_6YDW_014No text annotation
HL_6YDW_015Externally structured
HL_6YDW_017Pseudoknot geometry
HL_6YDW_018No text annotation
HL_6YDW_019T-loop with 2 stacked bulged bases
HL_6YDW_020No text annotation
HL_6YDW_021No text annotation
HL_6YDW_023tRNA D-loop
HL_6YDW_025No text annotation
HL_6YDW_072No text annotation
HL_6YDW_026No text annotation
HL_6YDW_027tRNA anticodon loop
HL_6YDW_028No text annotation
HL_6YDW_073No text annotation
HL_6YDW_035No text annotation
HL_6YDW_071No text annotation
HL_6YDW_043GNRA wlth tandem sheared
HL_6YDW_051No text annotation
HL_6YDW_068tRNA D-loop
HL_6YDW_070No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6YDW_0011/AA/3:5,
1/AA/21:22		No text annotation
IL_6YDW_0021/AA/39:40,
1/AA/215:217		Single bulged A
geometric
IL_5J7L_002
NA
IL_6YDW_0031/AA/44:46,
1/AA/178:179		Single bulged A
geometric
IL_6WPI_001
IL_14190.2
IL_6YDW_0041/AA/48:50,
1/AA/175:176		Minor groove platform
geometric
IL_4LFB_004
IL_34520.3
IL_6YDW_0051/AA/78:79,
1/AA/103:105		Minor groove platform
geometric
IL_5ML7_009
IL_34520.3
IL_6YDW_0071/AA/110:115,
1/AA/135:142		Kink-turn with non-sequential stacking
geometric
IL_6CZR_123
NA
IL_6YDW_0081/AA/116:119,
1/AA/133:134		Major groove platform; stack outside cWW
geometric
IL_1NTA_003
IL_74641.2
IL_6YDW_1061/AA/116:120,
1/AA/131:134		No text annotation
IL_6YDW_0091/AA/119:120,
1/AA/131:133		No text annotation
IL_6YDW_0101/AA/186:189,
1/AA/210:212		Isolated non-canonical cWW pair
geometric
IL_3TD0_005
NA
IL_6YDW_0111/AA/190:194,
1/AA/208:209		C-loop
geometric
IL_5J7L_018
NA
IL_6YDW_0121/AA/194:195,
1/AA/206:208		Single bulged G
geometric
IL_5J7L_019
NA
IL_6YDW_0131/AA/226:228,
1/AA/269:271		Isolated non-canonical cWW pair
geometric
IL_4YHW_001
NA
IL_6YDW_0141/AA/230:239,
1/AA/264:267		No text annotation
IL_6YDW_0151/AA/241:247,
1/AA/254:262		Kink-turn related
geometric
IL_4V88_415
NA
IL_6YDW_0161/AA/290:296,
1/AA/484:485		Multiple bulged bases
geometric
IL_1R3E_002
IL_05670.1
IL_6YDW_0171/AA/301:305,
1/AA/397:401		UAA/GAN
geometric
IL_4V9F_037
IL_08938.1
IL_6YDW_1071/AA/306:321,
1/AA/389:396		No text annotation
IL_6YDW_0181/AA/327:334,
1/AA/360:367		No text annotation
IL_6YDW_0191/AA/339:341,
1/AA/352:355		No text annotation
IL_6YDW_0201/AA/373:375,
1/AA/382:383		Other IL
geometric
IL_3WBM_004
IL_18188.1
IL_6YDW_0211/AA/414:418,
1/AA/444:445		Left turn
geometric
IL_5J7L_036
NA
IL_6YDW_0221/AA/419:423,
1/AA/439:443		tSH-tHW-tHS
geometric
IL_5J7L_037
NA
IL_6YDW_0231/AA/491:500,
1/AA/507:514		10x8 Sarcin-Ricin; G-bulge
geometric
IL_6UFH_002
IL_22278.1
IL_6YDW_0241/AA/526:527,
1/AA/837:839		Single bulged A
geometric
IL_5J7L_039
NA
IL_6YDW_0251/AA/529:531,
1/AA/834:835		Single bulged G
geometric
IL_4V88_442
NA
IL_6YDW_0281/AA/608:610,
1/AA/693:694		Single bulged C
geometric
IL_1S03_006
IL_05642.3
IL_6YDW_0331/AA/628:632,
1/AA/652:656		Double sheared with non-canonical cWW
geometric
IL_5J7L_274
NA
IL_6YDW_0341/AA/633:634,
1/AA/643:651		Major groove intercalation
geometric
IL_1U9S_003
IL_71421.3
IL_6YDW_0361/AA/843:845,
1/AA/927:930		No text annotation
geometric
IL_5J7L_058
NA
IL_6YDW_0371/AA/845:848,
1/AA/923:927		No text annotation
geometric
IL_8C3A_471
NA
IL_6YDW_0381/AA/849:851,
1/AA/920:922		Isolated non-canonical cWW pair
geometric
IL_4E48_004
IL_01003.4
IL_6YDW_0391/AA/851:855,
1/AA/915:920		No text annotation
IL_6YDW_0401/AA/857:859,
1/AA/911:913		Isolated non-canonical cWW pair
geometric
IL_4LFB_061
NA
IL_6YDW_0411/AA/860:863,
1/AA/907:910		Double sheared
geometric
IL_6CZR_169
NA
IL_6YDW_0461/BA/2:4,
1/BA/147:152		No text annotation
IL_6YDW_0471/BA/4:8,
1/BA/132:147		No text annotation
IL_6YDW_0491/BA/70:73,
1/BA/92:95		Tandem non-canonical cWW pairs
geometric
IL_3R2D_002
IL_71194.2
IL_6YDW_0501/BA/73:79,
1/BA/87:92		7x6 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_251
NA
IL_6YDW_0511/BA/181:183,
1/BA/192:194		Isolated non-canonical cWW pair
geometric
IL_3SZX_001
IL_01003.4
IL_6YDW_0521/BA/214:216,
1/BA/230:232		Isolated non-canonical cWW pair
geometric
IL_1YZ9_002
IL_01003.4
IL_6YDW_0531/BA/216:219,
1/BA/226:230		No text annotation
IL_6YDW_0541/BA/240:242,
1/BA/353:355		Isolated non-canonical cWW pair
geometric
IL_4WF9_020
IL_01003.4
IL_6YDW_0551/BA/242:246,
1/BA/346:353		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_6YDW_0561/BA/249:251,
1/BA/341:343		Isolated non-canonical cWW pair
geometric
IL_5VCI_002
IL_01003.4
IL_6YDW_0571/BA/259:261,
1/BA/316:318		Isolated non-canonical cWW pair
geometric
IL_6IA2_002
IL_01003.4
IL_6YDW_0581/BA/265:266,
1/BA/310:312		Single bulged A
geometric
IL_4V9F_025
IL_14190.2
IL_6YDW_0591/BA/285:288,
1/BA/303:305		Major groove platform with extra cWW
geometric
IL_7A0S_019
IL_36931.2
IL_6YDW_0601/BA/322:324,
1/BA/334:338		Multiple bulged bases
geometric
IL_4V9F_030
IL_57881.1
IL_6YDW_0611/BA/394:400,
1/BA/411:417		No text annotation
geometric
IL_5XWG_002
IL_74768.1
IL_6YDW_0621/BA/478:480,
1/BA/588:589		Single bulged A
geometric
IL_1NBS_005
IL_14190.2
IL_6YDW_0631/BA/502:504,
1/BA/524:526		Isolated cWH basepair
geometric
IL_2W2H_002
NA
IL_6YDW_0641/BA/504:507,
1/BA/521:524		No text annotation
geometric
IL_5D8H_002
IL_28482.1
IL_6YDW_0651/BA/531:534,
1/BA/545:546		Major groove platform
geometric
IL_3OXE_003
IL_48076.8
IL_6YDW_0661/BA/640:647,
1/BA/1006:1012		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_289
NA
IL_6YDW_0671/BA/663:666,
1/BA/773:779		No text annotation
IL_6YDW_0681/BA/682:687,
1/BA/694:697		C-loop
homologous
IL_9DFE_050
IL_63596.12
IL_6YDW_0691/BA/710:713,
1/BA/743:751		No text annotation
IL_6YDW_0701/BA/719:731,
1/BA/734:737		No text annotation
IL_6YDW_0711/BA/787:792,
1/BA/998:1000		No text annotation
IL_6YDW_0721/BA/798:800,
1/BA/990:992		Isolated tWW turn
geometric
IL_4WF9_063
IL_10432.1
IL_6YDW_0731/BA/801:804,
1/BA/988:989		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_6YDW_1101/BA/801:809,
1/BA/985:989		No text annotation
geometric
IL_8C3A_484
NA
IL_6YDW_0741/BA/804:809,
1/BA/985:988		Intercalated tWH
geometric
IL_5TBW_077
NA
IL_6YDW_0751/BA/809:817,
1/BA/982:985		No text annotation
IL_6YDW_1111/BA/809:818,
1/BA/981:985		No text annotation
IL_6YDW_0761/BA/822:823,
1/BA/975:977		Single bulged A
geometric
IL_4V9F_064
IL_14190.2
IL_6YDW_0771/BA/873:874,
1/BA/969:971		Single stack bend
geometric
IL_5J7L_032
NA
IL_6YDW_0781/BA/880:883,
1/BA/898:899		Minor groove platform, major groove intercalation
geometric
IL_5J7L_314
NA
IL_6YDW_0791/BA/884:885,
1/BA/894:897		Stack outside cWW
geometric
IL_6JQ6_004
IL_77710.1
IL_6YDW_0811/BA/929:940,
1/BA/956:959		No text annotation
IL_6YDW_0821/BA/1045:1047,
1/BA/1440:1441		Major groove platform
geometric
IL_4WF9_091
IL_48076.8
IL_6YDW_0831/BA/1049:1051,
1/BA/1435:1438		No text annotation
geometric
IL_4WF9_079
IL_80025.1
IL_6YDW_0841/BA/1062:1064,
1/BA/1265:1266		Single bulged U
geometric
IL_7RQB_080
NA
IL_6YDW_0851/BA/1065:1066,
1/BA/1261:1264		Minor groove platform
geometric
IL_7RQB_081
NA
IL_6YDW_0861/BA/1075:1078,
1/BA/1138:1140		No text annotation
geometric
IL_4P3T_002
NA
IL_6YDW_0871/BA/1080:1082,
1/BA/1134:1136		Isolated non-canonical cWW pair
geometric
IL_4V88_385
NA
IL_6YDW_0881/BA/1085:1087,
1/BA/1126:1131		No text annotation
IL_6YDW_1121/BA/1186:1191,
1/BA/1212:1222		No text annotation
IL_6YDW_1141/BA/1192:1194,
1/BA/1208:1211		No text annotation
geometric
IL_9DFE_030
IL_82096.1
IL_6YDW_0911/BA/1194:1196,
1/BA/1207:1208		Minor groove platform
geometric
IL_4LFB_004
IL_34520.3
IL_6YDW_0921/BA/1276:1277,
1/BA/1321:1323		Single stack bend
geometric
IL_4WF9_089
IL_15011.3
IL_6YDW_0931/BA/1277:1278,
1/BA/1319:1321		Major groove platform
geometric
IL_3OXE_003
IL_48076.8
IL_6YDW_0941/BA/1279:1282,
1/BA/1316:1318		No text annotation
geometric
IL_6DME_003
IL_75527.2
IL_6YDW_0951/BA/1282:1284,
1/BA/1312:1316		Major groove minor groove platform with extra cWW
geometric
IL_7A0S_086
IL_36931.2
IL_6YDW_0961/BA/1289:1293,
1/BA/1303:1307		Double sheared with non-canonical cWW
geometric
IL_5J7L_338
NA
IL_6YDW_0971/BA/1333:1335,
1/BA/1397:1401		Isolated non-canonical cWW with bulges
geometric
IL_7A0S_089
IL_68118.4
IL_6YDW_1131/BA/1333:1336,
1/BA/1394:1401		No text annotation
IL_6YDW_0981/BA/1335:1336,
1/BA/1394:1397		Multiple bulged bases
geometric
IL_7RQB_098
NA
IL_6YDW_0991/BA/1344:1346,
1/BA/1363:1367		No text annotation
IL_6YDW_1011/BA/1454:1461,
1/BA/1466:1472		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_6YDW_1021/BA/1483:1487,
1/BA/1497:1499		C-loop
geometric
IL_4JRC_003
IL_63596.12
IL_6YDW_1031/BA/1487:1489,
1/BA/1495:1497		Isolated non-canonical cWW pair
geometric
IL_6IA2_005
IL_01003.4
IL_6YDW_1041/BA/1507:1513,
1/BA/1533:1539		No text annotation

Problematic loops

#loop idProblemSequence
IL_6YDW_006Double sheared with non-canonical cWW
IL_6YDW_026No text annotation
IL_6YDW_027Minor groove platform
IL_6YDW_108No text annotation
IL_6YDW_029Isolated cWS basepair
IL_6YDW_030Minor groove platform
IL_6YDW_031Single bulged A
IL_6YDW_032Isolated non-canonical cWW pair
IL_6YDW_035No text annotation
IL_6YDW_042No text annotation
IL_6YDW_043No text annotation
IL_6YDW_044Isolated non-canonical cWW pair
IL_6YDW_045No text annotation
IL_6YDW_048Single bulged C
IL_6YDW_109No text annotation
IL_6YDW_080Multiple bulged bases
IL_6YDW_089Single stack bend
IL_6YDW_090No text annotation
IL_6YDW_100Single bulged A
IL_6YDW_105No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6YDW_0011/AA/31:34,
1/AA/222:226,
1/AA/271:274		No text annotation
J3_6YDW_0021/AA/41:44,
1/AA/179:186,
1/AA/212:214		No text annotation
J3_6YDW_0031/AA/326:327,
1/AA/367:373,
1/AA/383:384		No text annotation
J3_6YDW_0051/AA/561:567,
1/AA/578:589,
1/AA/706:709		No text annotation
J3_6YDW_0161/AA/623:632,
1/AA/652:663,
1/AA/671:678		No text annotation
J3_6YDW_0171/BA/8:11,
1/BA/106:120,
1/BA/127:132		No text annotation
J3_6YDW_0181/BA/14:54,
1/BA/61:70,
1/BA/95:102		No text annotation
J3_6YDW_0091/BA/251:257,
1/BA/320:322,
1/BA/338:341		No text annotation
geometric
J3_5J7L_038
NA
J3_6YDW_0101/BA/266:268,
1/BA/279:283,
1/BA/307:310		No text annotation
geometric
J3_8VTW_002
NA
J3_6YDW_0191/BA/482:504,
1/BA/524:531,
1/BA/546:586		No text annotation
J3_6YDW_0111/BA/669:676,
1/BA/755:759,
1/BA/768:770		No text annotation
J3_6YDW_0121/BA/676:678,
1/BA/701:708,
1/BA/753:755		No text annotation
J3_6YDW_0201/BA/1182:1183,
1/BA/1225:1236,
1/BA/1245:1251		No text annotation
J3_6YDW_0131/BA/1186:1187,
1/BA/1190:1191,
1/BA/1212:1222		No text annotation
J3_6YDW_0141/BA/1340:1343,
1/BA/1368:1370,
1/BA/1384:1390		No text annotation
geometric
J3_4WF9_009
J3_32601.6
J4_6YDW_0011/AA/52:55,
1/AA/62:69,
1/AA/156:158,
1/AA/167:173		No text annotation
J4_6YDW_0021/AA/71:77,
1/AA/106:108,
1/AA/144:147,
1/AA/153:154		No text annotation
J4_6YDW_0031/AA/296:298,
1/AA/404:409,
1/AA/450:461,
1/AA/483:484		No text annotation
homologous
J4_5J7L_003
NA
J4_6YDW_0041/AV/7:10,
1/AV/22:24,
1/AV/40:48,
1/AV/57:61		No text annotation
J4_6YDW_0061/BA/648:651,
1/BA/660:661,
1/BA/781:784,
1/BA/1003:1005		No text annotation
J4_6YDW_0071/BA/669:678,
1/BA/701:708,
1/BA/753:759,
1/BA/768:770		No text annotation
J4_6YDW_0081/BA/824:828,
1/BA/840:845,
1/BA/869:874,
1/BA/969:974		No text annotation
J4_6YDW_0091/BA/876:878,
1/BA/901:902,
1/BA/919:928,
1/BA/962:967		No text annotation
homologous
J4_9DFE_008
J4_42306.1
J4_6YDW_0101/BA/1446:1448,
1/BA/1478:1479,
1/BA/1503:1505,
1/BA/1541:1543		No text annotation
J4_6YDW_0111/BB/7:10,
1/BB/26:28,
1/BB/44:49,
1/BB/62:63		tRNA junction
homologous
J4_7UQ6_001
J4_95067.1
J5_6YDW_0011/BA/201:210,
1/BA/236:239,
1/BA/356:359,
1/BA/605:609,
1/BA/624:634		No text annotation
J5_6YDW_0021/BA/1052:1059,
1/BA/1269:1276,
1/BA/1323:1331,
1/BA/1403:1411,
1/BA/1429:1434		No text annotation
J5_6YDW_0031/BA/1069:1072,
1/BA/1143:1146,
1/BA/1158:1159,
1/BA/1181:1182,
1/BA/1251:1258		No text annotation
homologous
J5_7A0S_007
J5_39529.2
J6_6YDW_0031/BA/363:369,
1/BA/380:384,
1/BA/427:434,
1/BA/457:461,
1/BA/470:475,
1/BA/592:601		No text annotation
J6_6YDW_0021/BA/1069:1072,
1/BA/1143:1146,
1/BA/1158:1159,
1/BA/1181:1183,
1/BA/1225:1236,
1/BA/1245:1258		No text annotation

Problematic loops

#loop idProblemSequence
J3_6YDW_015No text annotation
J3_6YDW_004No text annotation
J3_6YDW_006No text annotation
J3_6YDW_007No text annotation
J3_6YDW_008No text annotation
J4_6YDW_012No text annotation
J4_6YDW_005No text annotation
J6_6YDW_001No text annotation

Coloring options:
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