RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6PPF_0011/A/67:74No text annotation
geometric
HL_4WF9_001
HL_08550.2
HL_6PPF_0021/A/87:95Pseudoknot geometry
homologous
HL_4WF9_002
HL_00911.3
HL_6PPF_0031/A/122:127No text annotation
homologous
HL_4WF9_003
HL_75660.9
HL_6PPF_0041/A/136:143GNRA with tandem sheared
homologous
HL_4WF9_004
HL_98423.4
HL_6PPF_0051/A/159:169No text annotation
homologous
HL_5J7L_138
NA
HL_6PPF_0061/A/191:211No text annotation
HL_6PPF_0071/A/228:233No text annotation
homologous
HL_7A0S_007
HL_91813.1
HL_6PPF_0081/A/249:255No text annotation
homologous
HL_4WF9_008
HL_76371.3
HL_6PPF_0101/A/349:356T-loop with 2 stacked bulged bases
homologous
HL_4WF9_010
HL_13999.4
HL_6PPF_0111/A/363:367No text annotation
homologous
HL_5J7L_143
NA
HL_6PPF_0121/A/371:379T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_6PPF_0131/A/429:439No text annotation
homologous
HL_5J7L_145
NA
HL_6PPF_0141/A/457:464No text annotation
homologous
HL_7RQB_014
NA
HL_6PPF_0151/A/509:514GNRA
homologous
HL_7A0S_015
HL_34789.5
HL_6PPF_0161/A/534:539GNRA
homologous
HL_7RQB_016
NA
HL_6PPF_0171/A/588:595No text annotation
homologous
HL_4WF9_017
HL_50318.1
HL_6PPF_0671/A/608:621No text annotation
HL_6PPF_0181/A/610:619T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_6PPF_0191/A/656:662GNRA related
geometric
HL_5J7L_179
NA
HL_6PPF_0201/A/675:680GNRA
homologous
HL_7RQB_020
NA
HL_6PPF_0211/A/687:693No text annotation
homologous
HL_7RQB_021
NA
HL_6PPF_0231/A/791:800No text annotation
homologous
HL_8VTW_022
NA
HL_6PPF_0241/A/826:832UNCG variation
homologous
HL_7A0S_023
HL_91813.1
HL_6PPF_0251/A/873:878No text annotation
homologous
HL_5J7L_157
NA
HL_6PPF_0281/A/1024:1031No text annotation
homologous
HL_5J7L_160
NA
HL_6PPF_0321/A/1262:1267GNRA
homologous
HL_7A0S_031
HL_34789.5
HL_6PPF_0701/A/1320:1328T-loop with 2 stacked bulged bases
homologous
HL_4WF9_032
HL_33597.4
HL_6PPF_0341/A/1363:1369Pseudoknot geometry with 3' bulge
homologous
HL_4WF9_033
HL_49081.1
HL_6PPF_0351/A/1402:1407GNRA
homologous
HL_5J7L_167
NA
HL_6PPF_0711/A/1428:1437No text annotation
homologous
HL_4WF9_035
HL_77449.2
HL_6PPF_0371/A/1496:1507UNCG variation
geometric
HL_5J7L_200
NA
HL_6PPF_0381/A/1538:1544Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
NA
HL_6PPF_0401/A/1613:1616Mini UNCG
homologous
HL_7A0S_039
HL_90436.4
HL_6PPF_0411/A/1657:1664No text annotation
homologous
HL_4WF9_038
HL_28592.3
HL_6PPF_0421/A/1675:1681GNRA
homologous
HL_5J7L_174
NA
HL_6PPF_0431/A/1736:1741No text annotation
geometric
HL_7RQB_042
NA
HL_6PPF_0441/A/1764:1769No text annotation
homologous
HL_7RQB_043
NA
HL_6PPF_0451/A/1781:1785No text annotation
homologous
HL_7RQB_044
NA
HL_6PPF_0461/A/1835:1840GNRA related
homologous
HL_5J7L_179
NA
HL_6PPF_0501/A/2238:2244No text annotation
homologous
HL_5J7L_185
NA
HL_6PPF_0721/A/2292:2306No text annotation
HL_6PPF_0731/A/2353:2360Pseudoknot geometry
homologous
HL_4WF9_052
HL_52651.3
HL_6PPF_0551/A/2384:2391GNRA with extra cWW
homologous
HL_4WF9_053
HL_87268.3
HL_6PPF_0561/A/2403:2408GNRA
homologous
HL_4WF9_054
HL_34789.5
HL_6PPF_0691/A/2428:2446No text annotation
HL_6PPF_0571/A/2433:2442No text annotation
homologous
HL_4WF9_055
HL_51853.2
HL_6PPF_0591/A/2730:2735Ribsomal LSU H95
homologous
HL_4WF9_061
HL_12125.3
HL_6PPF_0621/A/2844:2852No text annotation
homologous
HL_5J7L_201
NA
HL_6PPF_0631/A/2881:2886GNRA
homologous
HL_7A0S_068
HL_34789.5

Problematic loops

#loop idProblemSequence
HL_6PPF_009No text annotation
HL_6PPF_066No text annotation
HL_6PPF_022No text annotation
HL_6PPF_026No text annotation
HL_6PPF_027GNRA
HL_6PPF_029No text annotation
HL_6PPF_030No text annotation
HL_6PPF_031No text annotation
HL_6PPF_033No text annotation
HL_6PPF_036No text annotation
HL_6PPF_039No text annotation
HL_6PPF_047No text annotation
HL_6PPF_048No text annotation
HL_6PPF_049No text annotation
HL_6PPF_068No text annotation
HL_6PPF_051No text annotation
HL_6PPF_052No text annotation
HL_6PPF_053No text annotation
HL_6PPF_054No text annotation
HL_6PPF_058GNRA
HL_6PPF_060No text annotation
HL_6PPF_061GNRA
HL_6PPF_064No text annotation
HL_6PPF_065No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6PPF_0011/A/24:30,
1/A/556:562		Triple sheared with non-canonical cWW
geometric
IL_4WF9_001
IL_22311.2
IL_6PPF_0021/A/36:37,
1/A/489:491		Single bulged A
homologous
IL_7RQB_002
NA
IL_6PPF_0951/A/43:44,
1/A/481:483		Minor groove platform
homologous
IL_7A0S_003
IL_34520.4
IL_6PPF_0801/A/56:76,
1/A/109:113		No text annotation
geometric
IL_5TBW_144
NA
IL_6PPF_0041/A/81:85,
1/A/97:104		Kink-turn
homologous
IL_4WF9_004
IL_71972.2
IL_6PPF_0051/A/152:153,
1/A/175:177		Single bulged A
homologous
IL_4WF9_006
IL_14190.3
IL_6PPF_0061/A/186:187,
1/A/215:217		Single stack bend
homologous
IL_4WF9_007
IL_15011.4
IL_6PPF_0071/A/241:248,
1/A/256:262		8x7 Sarcin-Ricin; G-bulge
homologous
IL_4WF9_009
IL_62167.4
IL_6PPF_0961/A/319:327,
1/A/400:401		No text annotation
IL_6PPF_0111/A/336:338,
1/A/387:391		No text annotation
homologous
IL_5J7L_254
NA
IL_6PPF_0121/A/344:346,
1/A/359:360		Single bulged A
geometric
IL_3MJA_001
NA
IL_6PPF_0131/A/528:531,
1/A/542:555		No text annotation
geometric
IL_4WF9_015
IL_44923.2
IL_6PPF_0971/A/582:585,
1/A/598:601		Double sheared
homologous
IL_4WF9_016
IL_58355.3
IL_6PPF_0151/A/608:610,
1/A/619:621		Isolated non-canonical cWW pair
geometric
IL_4V88_465
NA
IL_6PPF_0161/A/639:641,
1/A/707:709		Isolated non-canonical cWW pair
homologous
IL_4WF9_018
IL_71625.4
IL_6PPF_0171/A/650:654,
1/A/664:668		AAA cross-strand stack
homologous
IL_7RQB_016
NA
IL_6PPF_0181/A/719:721,
1/A/853:855		No text annotation
homologous
IL_7RQB_017
NA
IL_6PPF_0191/A/721:725,
1/A/846:853		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_6PPF_0201/A/744:745,
1/A/810:812		Single bulged A
geometric
IL_5J7L_261
NA
IL_6PPF_0211/A/749:750,
1/A/775:777		Single bulged G
homologous
IL_7RQB_020
NA
IL_6PPF_0831/A/749:754,
1/A/771:777		No text annotation
geometric
IL_4LFB_055
IL_57885.3
IL_6PPF_0221/A/750:754,
1/A/771:775		Triple sheared
geometric
IL_4WF9_024
IL_15190.3
IL_6PPF_0231/A/785:787,
1/A/804:805		Major groove platform
homologous
IL_4WF9_026
IL_48076.9
IL_6PPF_0241/A/884:885,
1/A/986:988		Single stack bend
homologous
IL_7RQB_024
NA
IL_6PPF_0251/A/891:895,
1/A/977:980		No text annotation
homologous
IL_4WF9_029
IL_01742.1
IL_6PPF_0841/A/899:911,
1/A/959:973		No text annotation
IL_6PPF_0261/A/911:915,
1/A/956:959		C-loop
homologous
IL_4WF9_033
IL_16301.2
IL_6PPF_0271/A/995:1000,
1/A/1009:1014		No text annotation
geometric
IL_6O5F_001
NA
IL_6PPF_0281/A/1040:1042,
1/A/1205:1206		Single bulged C
homologous
IL_5J7L_276
NA
IL_6PPF_0291/A/1044:1048,
1/A/1199:1203		UAA/GAN
homologous
IL_5J7L_277
NA
IL_6PPF_0301/A/1050:1057,
1/A/1196:1197		SSU/LSU pseudoknot
homologous
IL_5J7L_278
NA
IL_6PPF_0311/A/1057:1059,
1/A/1195:1196		Single bulged U
geometric
IL_5J7L_279
NA
IL_6PPF_0321/A/1064:1070,
1/A/1186:1190		Kink-turn related
homologous
IL_4WF9_039
IL_57188.6
IL_6PPF_0341/A/1077:1079,
1/A/1168:1169		Single stack bend
geometric
IL_5TBW_375
NA
IL_6PPF_0351/A/1089:1099,
1/A/1152:1158		No text annotation
IL_6PPF_0981/A/1237:1239,
1/A/1287:1290		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.6
IL_6PPF_0991/A/1243:1247,
1/A/1279:1283		Partly complementary
geometric
IL_7VYX_004
IL_71154.4
IL_6PPF_0381/A/1248:1255,
1/A/1274:1278		Kink-turn
homologous
IL_7A0S_043
IL_90775.2
IL_6PPF_0391/A/1259:1261,
1/A/1268:1270		Intercalated cWW
homologous
IL_7A0S_044
IL_53541.1
IL_6PPF_0401/A/1302:1309,
1/A/2040:2046		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_049
NA
IL_6PPF_0411/A/1358:1362,
1/A/1370:1372		C-loop
homologous
IL_7A0S_047
IL_06671.2
IL_6PPF_0421/A/1390:1394,
1/A/1415:1419		UAA/GAN
homologous
IL_4WF9_051
IL_89021.4
IL_6PPF_0431/A/1396:1400,
1/A/1409:1413		tSH-tWH-tHS
homologous
IL_4WF9_052
IL_05821.2
IL_6PPF_0441/A/1448:1450,
1/A/1637:1638		Minor groove platform
geometric
IL_4R4V_001
IL_34520.4
IL_6PPF_0451/A/1455:1462,
1/A/1629:1632		No text annotation
IL_6PPF_0461/A/1463:1467,
1/A/1625:1628		Other IL
homologous
IL_4WF9_054
IL_74317.1
IL_6PPF_1001/A/1478:1481,
1/A/1605:1609		No text annotation
IL_6PPF_1011/A/1483:1486,
1/A/1599:1603		tSH-tHW
homologous
IL_5J7L_297
NA
IL_6PPF_0491/A/1488:1490,
1/A/1595:1597		Isolated non-canonical cWW pair
geometric
IL_4E48_005
IL_01003.5
IL_6PPF_0501/A/1494:1496,
1/A/1507:1509		Isolated non-canonical cWW pair
geometric
IL_4ZC7_004
IL_01003.5
IL_6PPF_0881/A/1514:1529,
1/A/1552:1571		No text annotation
IL_6PPF_0511/A/1535:1537,
1/A/1545:1546		Single bulged A
homologous
IL_5J7L_302
NA
IL_6PPF_0521/A/1573:1576,
1/A/1590:1594		UAA/GAN variation
homologous
IL_5J7L_303
NA
IL_6PPF_0531/A/1696:1701,
1/A/2033:2035		No text annotation
homologous
IL_4WF9_062
IL_12566.5
IL_6PPF_0541/A/1708:1710,
1/A/2024:2026		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_6PPF_0551/A/1711:1714,
1/A/2022:2023		Major groove platform; stack outside cWW
homologous
IL_4WF9_064
IL_74641.3
IL_6PPF_0901/A/1711:1719,
1/A/2019:2023		No text annotation
homologous
IL_4WF9_117
IL_80252.2
IL_6PPF_0561/A/1714:1719,
1/A/2019:2022		Intercalated tWH
geometric
IL_7A0S_062
IL_28217.2
IL_6PPF_0571/A/1731:1736,
1/A/1741:1747		tSH-tSH-tHH-tHS
homologous
IL_7RQB_068
NA
IL_6PPF_0581/A/1756:1761,
1/A/1772:1776		tSH-tHW-tWW
geometric
IL_5J7L_022
NA
IL_6PPF_0591/A/1799:1800,
1/A/2009:2011		No text annotation
IL_6PPF_0601/A/1827:1833,
1/A/1842:1850		Kink-turn related
homologous
IL_7RQB_070
NA
IL_6PPF_0611/A/2079:2081,
1/A/2646:2647		Major groove platform
homologous
IL_5J7L_320
NA
IL_6PPF_0641/A/2231:2233,
1/A/2249:2250		Single bulged G
geometric
IL_8VFS_001
IL_28408.3
IL_6PPF_0661/A/2379:2382,
1/A/2393:2396		Double sheared
homologous
IL_5J7L_333
NA
IL_6PPF_0671/A/2429:2432,
1/A/2443:2445		No text annotation
IL_6PPF_0681/A/2665:2669,
1/A/2803:2811		tSH-tHS-tHW
homologous
IL_4WF9_099
IL_04638.4
IL_6PPF_0921/A/2709:2713,
1/A/2754:2756		C-loop
homologous
IL_7A0S_095
IL_63596.13
IL_6PPF_0711/A/2716:2720,
1/A/2747:2751		UAA/GAN related, with intercalation
homologous
IL_4WF9_102
IL_82016.1
IL_6PPF_0721/A/2724:2725,
1/A/2740:2743		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_6PPF_0731/A/2766:2771,
1/A/2791:2796		UAA/GAN with extra cWW
homologous
IL_5J7L_350
NA
IL_6PPF_0741/A/2863:2864,
1/A/2903:2905		Major groove intercalation
homologous
IL_5J7L_352
NA
IL_6PPF_0751/A/2868:2870,
1/A/2896:2899		No text annotation
homologous
IL_4WF9_107
IL_05502.1
IL_6PPF_0931/A/2870:2877,
1/A/2890:2896		No text annotation
IL_6PPF_0761/A/2872:2877,
1/A/2890:2894		tHS double platform
homologous
IL_4WF9_108
IL_48489.2
IL_6PPF_0771/B/15:16,
1/B/63:65		Major groove intercalation
homologous
IL_5J7L_355
NA
IL_6PPF_0791/B/32:36,
1/B/42:46		Symmetric double minor groove platform
geometric
IL_7RQB_114
NA
IL_6PPF_0941/B/69:81,
1/B/91:103		No text annotation

Problematic loops

#loop idProblemSequence
IL_6PPF_003Tandem non-canonical cWW pairs
IL_6PPF_081Single stack bend
IL_6PPF_008Major groove minor groove platform; mini C-loop
IL_6PPF_009No text annotation
IL_6PPF_010No text annotation
IL_6PPF_014Double sheared with non-canonical cWW
IL_6PPF_082No text annotation
IL_6PPF_085No text annotation
IL_6PPF_033No text annotation
IL_6PPF_086No text annotation
IL_6PPF_087Tandem non-canonical cWW pairs
IL_6PPF_036Tandem non-canonical cWW pairs
IL_6PPF_037No text annotation
IL_6PPF_047No text annotation
IL_6PPF_048No text annotation
IL_6PPF_089No text annotation
IL_6PPF_062No text annotation
IL_6PPF_091No text annotation
IL_6PPF_063Isolated tHS basepair with bulges
IL_6PPF_065Isolated tHS basepair with bulges
IL_6PPF_069Sarcin-Ricin target in LSU H95; G-bulge
IL_6PPF_070C-loop with extra cWW pair
IL_6PPF_102No text annotation
IL_6PPF_078No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6PPF_0221/A/30:31,
1/A/521:528,
1/A/555:556		No text annotation
homologous
J3_5J7L_036
NA
J3_6PPF_0151/A/32:35,
1/A/492:508,
1/A/515:520		No text annotation
homologous
J3_9DFE_003
J3_07616.2
J3_6PPF_0021/A/56:67,
1/A/74:76,
1/A/109:113		No text annotation
homologous
J3_4WF9_001
J3_47707.1
J3_6PPF_0161/A/272:276,
1/A/295:302,
1/A/416:417		No text annotation
homologous
J3_4WF9_022
J3_97971.2
J3_6PPF_0231/A/730:736,
1/A/820:824,
1/A/834:841		No text annotation
J3_6PPF_0051/A/745:747,
1/A/779:783,
1/A/807:810		No text annotation
homologous
J3_4WF9_003
J3_69816.2
J3_6PPF_0071/A/1337:1342,
1/A/1670:1672,
1/A/1684:1687		No text annotation
homologous
J3_7RQB_007
NA
J3_6PPF_0241/A/1337:1344,
1/A/1668:1672,
1/A/1684:1687		No text annotation
J3_6PPF_0081/A/1344:1348,
1/A/1650:1656,
1/A/1665:1668		No text annotation
homologous
J3_4WF9_005
J3_68164.1
J3_6PPF_0191/A/1383:1389,
1/A/1420:1424,
1/A/1441:1442		No text annotation
homologous
J3_9DFE_012
J3_94309.2
J3_6PPF_0201/A/1470:1475,
1/A/1612:1613,
1/A/1616:1622		No text annotation
homologous
J3_5J7L_069
NA
J3_6PPF_0101/A/2120:2122,
1/A/2225:2230,
1/A/2251:2257		No text annotation
homologous
J3_4WF9_007
J3_07703.1
J3_6PPF_0111/A/2324:2326,
1/A/2350:2352,
1/A/2361:2366		No text annotation
homologous
J3_4WF9_008
J3_05327.2
J3_6PPF_0121/A/2818:2820,
1/A/2831:2836,
1/A/2914:2918		No text annotation
homologous
J3_7RQB_013
NA
J3_6PPF_0131/A/2839:2840,
1/A/2856:2861,
1/A/2907:2911		No text annotation
homologous
J3_4WF9_021
J3_76911.2
J3_6PPF_0141/B/9:14,
1/B/66:68,
1/B/104:107		No text annotation
J4_6PPF_0011/A/271:272,
1/A/417:422,
1/A/446:453,
1/A/468:471		No text annotation
homologous
J4_5J7L_018
NA
J4_6PPF_0021/A/340:346,
1/A/359:363,
1/A/367:369,
1/A/381:385		No text annotation
J4_6PPF_0091/A/645:648,
1/A/670:674,
1/A/681:684,
1/A/696:703		No text annotation
homologous
J4_5J7L_020
NA
J4_6PPF_0101/A/1310:1315,
1/A/1333:1334,
1/A/1690:1693,
1/A/2038:2039		No text annotation
homologous
J4_4WF9_004
J4_64571.6
J4_6PPF_0051/A/1348:1353,
1/A/1377:1382,
1/A/1443:1444,
1/A/1642:1650		No text annotation
J4_6PPF_0061/A/1490:1492,
1/A/1511:1513,
1/A/1572:1573,
1/A/1594:1595		No text annotation
J4_6PPF_0071/A/2314:2318,
1/A/2372:2376,
1/A/2399:2401,
1/A/2410:2412		No text annotation
homologous
J4_4WF9_008
J4_98139.1
J4_6PPF_0111/A/2672:2675,
1/A/2703:2705,
1/A/2760:2764,
1/A/2798:2800		No text annotation
homologous
J4_9DFE_010
J4_77044.5
J5_6PPF_0051/A/47:54,
1/A/115:120,
1/A/129:130,
1/A/149:151,
1/A/178:180		No text annotation
homologous
J5_4WF9_001
J5_27223.2
J5_6PPF_0021/A/271:276,
1/A/295:302,
1/A/416:422,
1/A/446:453,
1/A/468:471		No text annotation
J5_6PPF_0061/A/628:633,
1/A/715:718,
1/A/856:859,
1/A/1236:1237,
1/A/1290:1296		No text annotation
homologous
J5_4WF9_004
J5_74302.6
J5_6PPF_0041/A/1719:1727,
1/A/1751:1752,
1/A/1780:1781,
1/A/1785:1793,
1/A/2017:2019		No text annotation
homologous
J5_4WF9_005
J5_99177.2
J6_6PPF_0011/A/45:46,
1/A/181:186,
1/A/217:227,
1/A/234:238,
1/A/265:269,
1/A/473:480		No text annotation
J6_6PPF_0021/A/2103:2106,
1/A/2272:2275,
1/A/2287:2288,
1/A/2310:2313,
1/A/2413:2424,
1/A/2450:2464		No text annotation
J7_6PPF_0021/A/864:869,
1/A/882:883,
1/A/989:992,
1/A/1017:1022,
1/A/1033:1037,
1/A/1209:1210,
1/A/1226:1231		No text annotation
J10_6PPF_0021/A/8:15,
1/A/571:579,
1/A/604:608,
1/A/621:623,
1/A/1301:1302,
1/A/2046:2052,
1/A/2069:2072,
1/A/2654:2659,
1/A/2817:2818,
1/A/2918:2919		No text annotation

Problematic loops

#loop idProblemSequence
J3_6PPF_001No text annotation
J3_6PPF_003No text annotation
J3_6PPF_004No text annotation
J3_6PPF_017No text annotation
J3_6PPF_006No text annotation
J3_6PPF_018No text annotation
J3_6PPF_009No text annotation
J3_6PPF_021No text annotation
J4_6PPF_003No text annotation
J4_6PPF_004No text annotation
J4_6PPF_008No text annotation
J5_6PPF_001No text annotation
J5_6PPF_003No text annotation
J7_6PPF_001No text annotation
J10_6PPF_001No text annotation

Coloring options:
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