RNA 3D Hub //

5NCO Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_5NCO_0221/A/744:753No text annotation
homologous
HL_7A0S_022
HL_50204.1
HL_5NCO_0301/A/1222:1227GNRA
homologous
HL_5J7L_164
NA
HL_5NCO_0491/A/2027:2036No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_5NCO_0611/A/2551:2557No text annotation
homologous
HL_4WF9_058
HL_48677.1
HL_5NCO_0671/A/2819:2827No text annotation
homologous
HL_5J7L_201
NA

Problematic loops

#loop idProblemSequence
HL_5NCO_001No text annotation
HL_5NCO_002No text annotation
HL_5NCO_003No text annotation
HL_5NCO_004No text annotation
HL_5NCO_071No text annotation
HL_5NCO_005No text annotation
HL_5NCO_006No text annotation
HL_5NCO_007No text annotation
HL_5NCO_008No text annotation
HL_5NCO_009No text annotation
HL_5NCO_010T-loop with 2 stacked bulged bases
HL_5NCO_011No text annotation
HL_5NCO_012T-loop with unstacked turn
HL_5NCO_013No text annotation
HL_5NCO_073No text annotation
HL_5NCO_014Pseudoknot geometry
HL_5NCO_015GNRA
HL_5NCO_016GNRA
HL_5NCO_017T-loop with 2 stacked bulged bases
HL_5NCO_018No text annotation
HL_5NCO_019GNRA
HL_5NCO_020No text annotation
HL_5NCO_021GNRA wlth tandem sheared
HL_5NCO_023No text annotation
HL_5NCO_024No text annotation
HL_5NCO_025GNRA
HL_5NCO_026No text annotation
HL_5NCO_027No text annotation
HL_5NCO_028GNRA wlth tandem sheared
HL_5NCO_029No text annotation
HL_5NCO_031T-loop with 2 stacked bulged bases
HL_5NCO_032Pseudoknot geometry with 3' bulge
HL_5NCO_033GNRA
HL_5NCO_034No text annotation
HL_5NCO_035Mini UNCG with extended bulge
HL_5NCO_036Pseudoknot geometry with 3' bulge
HL_5NCO_037UNCG
HL_5NCO_038No text annotation
HL_5NCO_039No text annotation
HL_5NCO_040GNRA
HL_5NCO_041No text annotation
HL_5NCO_042No text annotation
HL_5NCO_043No text annotation
HL_5NCO_044No text annotation
HL_5NCO_045GNRA related
HL_5NCO_046GNRA variation
HL_5NCO_047No text annotation
HL_5NCO_048No text annotation
HL_5NCO_050No text annotation
HL_5NCO_051No text annotation
HL_5NCO_052No text annotation
HL_5NCO_053No text annotation
HL_5NCO_054No text annotation
HL_5NCO_074No text annotation
HL_5NCO_055Pseudoknot geometry
HL_5NCO_056GNRA
HL_5NCO_057GNRA
HL_5NCO_058No text annotation
HL_5NCO_059No text annotation
HL_5NCO_060GNRA variation
HL_5NCO_062GNRA
HL_5NCO_063GNRA
HL_5NCO_064Ribsomal LSU H95
HL_5NCO_065No text annotation
HL_5NCO_066No text annotation
HL_5NCO_068GNRA
HL_5NCO_072No text annotation
HL_5NCO_069No text annotation
HL_5NCO_070Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_5NCO_0061/A/24:30,
1/A/510:516		Triple sheared with non-canonical cWW
geometric
IL_5J7L_245
NA
IL_5NCO_0121/A/239:245,
1/A/253:258		7x6 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_251
NA
IL_5NCO_0261/A/775:777,
1/A/787:791		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_5NCO_0531/A/1319:1323,
1/A/1331:1333		C-loop
homologous
IL_5J7L_291
NA
IL_5NCO_0741/A/1798:1804,
1/A/1813:1821		Kink-turn related
homologous
IL_5J7L_313
NA
IL_5NCO_0821/A/2054:2056,
1/A/2612:2615		No text annotation
homologous
IL_5J7L_321
NA
IL_5NCO_0831/A/2067:2069,
1/A/2442:2443		Single bulged U
homologous
IL_7A0S_075
IL_97561.2
IL_5NCO_1061/A/2687:2691,
1/A/2718:2722		UAA/GAN related, with intercalation
homologous
IL_5J7L_348
NA
IL_5NCO_1121/A/2843:2846,
1/A/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
NA
IL_5NCO_1181/B/71:79,
1/B/97:105		Bacterial 5S Loop E
homologous
IL_5J7L_359
NA

Problematic loops

#loop idProblemSequence
IL_5NCO_119No text annotation
IL_5NCO_001Single bulged U
IL_5NCO_002No text annotation
IL_5NCO_003Single bulged C
IL_5NCO_120No text annotation
IL_5NCO_004No text annotation
IL_5NCO_128No text annotation
IL_5NCO_005tSH-tHW-tHS-cWW
IL_5NCO_007Single bulged A
IL_5NCO_008Minor groove platform
IL_5NCO_009No text annotation
IL_5NCO_010Single stack bend
IL_5NCO_0118x7 Sarcin-Ricin; G-bulge
IL_5NCO_013No text annotation
IL_5NCO_014No text annotation
IL_5NCO_015No text annotation
IL_5NCO_016No text annotation
IL_5NCO_017Double sheared
IL_5NCO_018Isolated non-canonical cWW pair
IL_5NCO_019AAA cross-strand stack
IL_5NCO_020Isolated non-canonical cWW pair
IL_5NCO_021tHW-tHW cross-strand stack
IL_5NCO_022Single bulged A
IL_5NCO_023Single bulged G
IL_5NCO_024Triple sheared
IL_5NCO_025Major groove platform
IL_5NCO_027Single stack bend
IL_5NCO_02890 degree turn
IL_5NCO_121No text annotation
IL_5NCO_029Stack outside cWW
IL_5NCO_030No text annotation
IL_5NCO_0317x7 Sarcin-Ricin with intercalated A; G-bulge
IL_5NCO_032Single bulged G
IL_5NCO_033C-loop with bulged stacked A's
IL_5NCO_034Isolated non-canonical cWW pair
IL_5NCO_035Double sheared with non-canonical cWW
IL_5NCO_122No text annotation
IL_5NCO_036Isolated tHS basepair with bulges
IL_5NCO_037Single bulged C
IL_5NCO_038UAA/GAN
IL_5NCO_039SSU/LSU pseudoknot
IL_5NCO_040Single bulged U
IL_5NCO_041Kink-turn related
IL_5NCO_042No text annotation
IL_5NCO_043Isolated non-canonical cWW pair
IL_5NCO_044Tandem non-canonical cWW pairs
IL_5NCO_045Kink-turn
IL_5NCO_046No text annotation
IL_5NCO_047Major groove platform
IL_5NCO_048Isolated cWS basepair
IL_5NCO_049No text annotation
IL_5NCO_050Kink-turn
IL_5NCO_0518x7 Sarcin-Ricin; G-bulge
IL_5NCO_052Major groove platform; stack outside cWW
IL_5NCO_054UAA/GAN
IL_5NCO_055tSH-tHW-tHS
IL_5NCO_056No text annotation
IL_5NCO_057UAA/GAN
IL_5NCO_058Tandem non-canonical cWW pairs
IL_5NCO_059tSH-tHW
IL_5NCO_060Single bulged U
IL_5NCO_061No text annotation
IL_5NCO_062tSH-tHW-tHS
IL_5NCO_063180 degree turn
IL_5NCO_064Major groove platform
IL_5NCO_065UAA/GAN variation
IL_5NCO_066No text annotation
IL_5NCO_067Isolated tWW turn
IL_5NCO_068Major groove platform; stack outside cWW
IL_5NCO_123No text annotation
IL_5NCO_069Intercalated tWH
IL_5NCO_070tSH-tSH-tHH-tHS
IL_5NCO_0716x5 Sarcin-Ricin; G-bulge
IL_5NCO_072Triple sheared
IL_5NCO_073Single bulged A
IL_5NCO_075Minor groove platform, major groove intercalation
IL_5NCO_076Major groove intercalation
IL_5NCO_077Major groove minor groove platform; mini C-loop
IL_5NCO_124No text annotation
IL_5NCO_078UAA/GAN related
IL_5NCO_079Bulged stacked bases
IL_5NCO_080No text annotation
IL_5NCO_081Major groove platform
IL_5NCO_084Minor groove platform
IL_5NCO_085Isolated tHS basepair with bulges
IL_5NCO_086No text annotation
IL_5NCO_125No text annotation
IL_5NCO_129No text annotation
IL_5NCO_126Kink-turn
IL_5NCO_087Kink-turn related
IL_5NCO_088Kink-turn
IL_5NCO_127No text annotation
IL_5NCO_089Single bulged U
IL_5NCO_090No text annotation
IL_5NCO_091Double sheared
IL_5NCO_092Single bulged U
IL_5NCO_093Single stack bend
IL_5NCO_094Major groove platform
IL_5NCO_095Major groove platform
IL_5NCO_096Major groove minor groove platform with extra cWW
IL_5NCO_097Double sheared with non-canonical cWW
IL_5NCO_098Major groove platform
IL_5NCO_099Isolated non-canonical cWW with bulges
IL_5NCO_100No text annotation
IL_5NCO_101Major groove platform with intercalation
IL_5NCO_102Single bulged A
IL_5NCO_103tSH-tHS-tHW
IL_5NCO_104Sarcin-Ricin target in LSU H95; G-bulge
IL_5NCO_105C-loop
IL_5NCO_107Multiple bulged bases
IL_5NCO_108UAA/GAN with extra cWW
IL_5NCO_109Single bulged A
IL_5NCO_110No text annotation
IL_5NCO_111Major groove intercalation
IL_5NCO_113tHS double platform
IL_5NCO_114Major groove intercalation
IL_5NCO_115No text annotation
IL_5NCO_116Major groove minor groove platform; mini C-loop
IL_5NCO_117Symmetric double minor groove platform

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_5NCO_0161/A/32:35,
1/A/445:461,
1/A/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_5NCO_0031/A/683:689,
1/A/773:775,
1/A/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_5NCO_0061/A/1298:1303,
1/A/1625:1627,
1/A/1639:1642		No text annotation
homologous
J3_5J7L_041
NA
J4_5NCO_0011/A/268:269,
1/A/370:375,
1/A/399:406,
1/A/421:424		No text annotation
homologous
J4_5J7L_018
NA
J4_5NCO_0031/A/601:604,
1/A/624:628,
1/A/635:638,
1/A/650:656		No text annotation
homologous
J4_5J7L_020
NA
J5_5NCO_0021/A/531:533,
1/A/560:564,
1/A/577:579,
1/A/1261:1262,
1/A/2017:2018		No text annotation
homologous
J5_5J7L_014
NA
J7_5NCO_0011/A/8:15,
1/A/525:531,
1/A/2018:2023,
1/A/2040:2043,
1/A/2625:2630,
1/A/2788:2789,
1/A/2894:2895		No text annotation

Problematic loops

#loop idProblemSequence
J3_5NCO_001No text annotation
J3_5NCO_015No text annotation
J3_5NCO_002No text annotation
J3_5NCO_004No text annotation
J3_5NCO_005No text annotation
J3_5NCO_007No text annotation
J3_5NCO_008No text annotation
J3_5NCO_017No text annotation
J3_5NCO_009Kink-turn 3-way junction
J3_5NCO_018No text annotation
J3_5NCO_010No text annotation
J3_5NCO_019No text annotation
J3_5NCO_011No text annotation
J3_5NCO_012No text annotation
J3_5NCO_013No text annotation
J3_5NCO_014No text annotation
J4_5NCO_002No text annotation
J4_5NCO_004No text annotation
J4_5NCO_005No text annotation
J4_5NCO_006No text annotation
J4_5NCO_007No text annotation
J4_5NCO_008No text annotation
J4_5NCO_009No text annotation
J4_5NCO_010No text annotation
J4_5NCO_011No text annotation
J5_5NCO_007No text annotation
J5_5NCO_001No text annotation
J5_5NCO_003No text annotation
J5_5NCO_004No text annotation
J5_5NCO_008No text annotation
J5_5NCO_005No text annotation
J5_5NCO_006No text annotation
J6_5NCO_001No text annotation
J7_5NCO_002No text annotation

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