RNA 3D Hub //

1FFK Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_1FFK_0171/0/670:676No text annotation
homologous
HL_4V9F_019
HL_41169.1
HL_1FFK_0531/0/2298:2310No text annotation
homologous
HL_4V9F_056
HL_02042.1

Problematic loops

#loop idProblemSequence
HL_1FFK_001Pseudoknot with intercalation
HL_1FFK_002Pseudoknot geometry
HL_1FFK_003No text annotation
HL_1FFK_004No text annotation
HL_1FFK_005No text annotation
HL_1FFK_006No text annotation
HL_1FFK_007No text annotation
HL_1FFK_008GNRA
HL_1FFK_009T-loop with 2 stacked bulged bases
HL_1FFK_010T-loop with unstacked turn
HL_1FFK_011No text annotation
HL_1FFK_012Pseudoknot geometry
HL_1FFK_013GNRA
HL_1FFK_014GNRA
HL_1FFK_015GNRA
HL_1FFK_016T-loop with 2 stacked bulged bases
HL_1FFK_018GNRA
HL_1FFK_019Mini UNCG
HL_1FFK_020GNRA
HL_1FFK_021GNRA
HL_1FFK_022No text annotation
HL_1FFK_023No text annotation
HL_1FFK_024No text annotation
HL_1FFK_025No text annotation
HL_1FFK_026GNRA
HL_1FFK_027No text annotation
HL_1FFK_028No text annotation
HL_1FFK_029Anticodon loop related
HL_1FFK_030GNRA
HL_1FFK_031T-loop with 2 stacked bulged bases
HL_1FFK_032Pseudoknot geometry with 3' bulge
HL_1FFK_033GNRA
HL_1FFK_034No text annotation
HL_1FFK_035No text annotation
HL_1FFK_036Other HL
HL_1FFK_037GNRA
HL_1FFK_038Mini UNCG
HL_1FFK_039No text annotation
HL_1FFK_040GNRA wlth tandem sheared
HL_1FFK_041UNCG
HL_1FFK_042GNRA
HL_1FFK_043No text annotation
HL_1FFK_044No text annotation
HL_1FFK_045GNRA
HL_1FFK_046GNRA related
HL_1FFK_047No text annotation
HL_1FFK_048No text annotation
HL_1FFK_049No text annotation
HL_1FFK_050No text annotation
HL_1FFK_051GNRA
HL_1FFK_052No text annotation
HL_1FFK_054No text annotation
HL_1FFK_055Pseudoknot geometry
HL_1FFK_056No text annotation
HL_1FFK_057GNRA
HL_1FFK_058Pseudoknot geometry
HL_1FFK_059No text annotation
HL_1FFK_060GNRA variation
HL_1FFK_061tRNA D-loop
HL_1FFK_070No text annotation
HL_1FFK_062GNRA
HL_1FFK_063GNRA
HL_1FFK_064Ribsomal LSU H95
HL_1FFK_065No text annotation
HL_1FFK_066No text annotation
HL_1FFK_067GNRA
HL_1FFK_071No text annotation
HL_1FFK_068No text annotation
HL_1FFK_069GNRA

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_1FFK_0311/0/936:940,
1/0/1026:1034		Kink-turn
homologous
IL_4V9F_031
IL_94910.1
IL_1FFK_0331/0/952:956,
1/0/1011:1015		5x5 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_4V9F_033
IL_38862.5
IL_1FFK_0501/0/1456:1460,
1/0/1483:1489		UAA/GAN
homologous
IL_4V9F_052
IL_82787.1
IL_1FFK_1051/0/1744:1752,
1/0/2031:2035		No text annotation
homologous
IL_4V9F_111
IL_80252.1
IL_1FFK_0601/0/1747:1752,
1/0/2031:2034		Intercalated tWH
homologous
IL_4V9F_062
IL_28217.1
IL_1FFK_0811/0/2501:2505,
1/0/2515:2519		Double sheared with non-canonical cWW
homologous
IL_4V9F_085
IL_87767.1

Problematic loops

#loop idProblemSequence
IL_1FFK_001Triple sheared with non-canonical cWW
IL_1FFK_002Single bulged A
IL_1FFK_003Major groove platform with extra cWW
IL_1FFK_004Kink-turn
IL_1FFK_005Single stack bend
IL_1FFK_0068x7 Sarcin-Ricin; G-bulge
IL_1FFK_0077x6 Sarcin-Ricin; G-bulge
IL_1FFK_008Major groove platform; stack outside cWW
IL_1FFK_103Kink-turn with embedded cWW pair
IL_1FFK_009No text annotation
IL_1FFK_010Single bulged G
IL_1FFK_011No text annotation
IL_1FFK_012Tandem non-canonical cWW pairs
IL_1FFK_0138x7 Sarcin-Ricin with CC bifurcated pair; G-bulge
IL_1FFK_014Single bulged U
IL_1FFK_015No text annotation
IL_1FFK_016No text annotation
IL_1FFK_017No text annotation
IL_1FFK_018Tandem non-canonical cWW pairs
IL_1FFK_019Triple sheared related
IL_1FFK_0207x6 Sarcin-Ricin; G-bulge
IL_1FFK_021AAA cross-strand stack
IL_1FFK_022Multiple bulged bases
IL_1FFK_023tSH-tHW-tHS
IL_1FFK_024Isolated non-canonical cWW pair
IL_1FFK_025tHW-tHW cross-strand stack
IL_1FFK_026Single bulged G
IL_1FFK_027Triple sheared
IL_1FFK_028Major groove platform with extra cWW
IL_1FFK_029Single bulged U
IL_1FFK_030Multiple bulged bases
IL_1FFK_032Single bulged A
IL_1FFK_034Minor groove platform
IL_1FFK_035No text annotation
IL_1FFK_036No text annotation
IL_1FFK_037UAA/GAN
IL_1FFK_038SSU/LSU pseudoknot
IL_1FFK_039Single bulged U
IL_1FFK_040Kink-turn related
IL_1FFK_104No text annotation
IL_1FFK_041Single bulged G
IL_1FFK_042Kink-turn
IL_1FFK_043Bulged stacked bases
IL_1FFK_044Isolated cWS basepair
IL_1FFK_045Isolated non-canonical cWW pair
IL_1FFK_046Kink-turn
IL_1FFK_0477x6 Sarcin-Ricin; G-bulge
IL_1FFK_048Major groove platform; stack outside cWW
IL_1FFK_049C-loop
IL_1FFK_051No text annotation
IL_1FFK_052No text annotation
IL_1FFK_053tSH-tHW-tHS
IL_1FFK_054tSH-tHH-tHS
IL_1FFK_055No text annotation
IL_1FFK_056Kink-turn
IL_1FFK_057No text annotation
IL_1FFK_058Isolated tWW turn
IL_1FFK_059Major groove platform; stack outside cWW
IL_1FFK_061tSH-tSH-tHH-tHS
IL_1FFK_062Single bulged A
IL_1FFK_063Kink-turn related
IL_1FFK_064Minor groove platform, major groove intercalation
IL_1FFK_065Major groove intercalation
IL_1FFK_066Major groove minor groove platform; mini C-loop
IL_1FFK_067No text annotation
IL_1FFK_068Bulged stacked bases
IL_1FFK_069No text annotation
IL_1FFK_070No text annotation
IL_1FFK_071No text annotation
IL_1FFK_072Single bulged U
IL_1FFK_073Minor groove platform
IL_1FFK_074Isolated tHS basepair with bulges
IL_1FFK_075Single bulged A
IL_1FFK_076Isolated tHS basepair with bulges
IL_1FFK_077Single stack bend
IL_1FFK_078Major groove platform
IL_1FFK_079Major groove platform
IL_1FFK_080Major groove minor groove platform with extra cWW
IL_1FFK_082Major groove platform
IL_1FFK_083Isolated non-canonical cWW with bulges
IL_1FFK_084Multiple bulged bases
IL_1FFK_085Major groove platform with intercalation
IL_1FFK_086Single bulged A
IL_1FFK_087No text annotation
IL_1FFK_088Sarcin-Ricin target in LSU H95; G-bulge
IL_1FFK_089C-loop
IL_1FFK_090UAA/GAN variation
IL_1FFK_091Bulged stacked bases
IL_1FFK_092UAA/GAN with extra cWW
IL_1FFK_093Isolated non-canonical cWW with bulges
IL_1FFK_094Single bulged A
IL_1FFK_095tHS double platform
IL_1FFK_096Double sheared
IL_1FFK_097Major groove intercalation
IL_1FFK_098No text annotation
IL_1FFK_099Major groove minor groove platform; mini C-loop
IL_1FFK_100Symmetric double minor groove platform
IL_1FFK_1017x6 Sarcin-Ricin; G-bulge
IL_1FFK_102Single bulged U

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_1FFK_0131/0/52:53,
1/0/66:72,
1/0/105:109		No text annotation
homologous
J3_4V9F_014
J3_01004.1
J3_1FFK_0141/0/302:307,
1/0/323:332,
1/0/344:349		No text annotation
homologous
J3_4V9F_015
J3_59706.1
J4_1FFK_0021/0/1374:1382,
1/0/1400:1401,
1/0/1721:1725,
1/0/2050:2051		No text annotation
homologous
J4_4V9F_003
J4_75426.1
J5_1FFK_0061/0/1752:1760,
1/0/1784:1785,
1/0/1807:1808,
1/0/1812:1820,
1/0/2029:2031		No text annotation
homologous
J5_4V9F_006
J5_99177.1

Problematic loops

#loop idProblemSequence
J3_1FFK_010No text annotation
J3_1FFK_011No text annotation
J3_1FFK_012No text annotation
J3_1FFK_001No text annotation
J3_1FFK_002No text annotation
J3_1FFK_003No text annotation
J3_1FFK_004No text annotation
J3_1FFK_005No text annotation
J3_1FFK_015No text annotation
J3_1FFK_016No text annotation
J3_1FFK_006No text annotation
J3_1FFK_017No text annotation
J3_1FFK_007No text annotation
J3_1FFK_008No text annotation
J3_1FFK_018No text annotation
J3_1FFK_0095S rRNA junction
J4_1FFK_001No text annotation
J4_1FFK_003No text annotation
J4_1FFK_004No text annotation
J4_1FFK_005No text annotation
J4_1FFK_006No text annotation
J4_1FFK_007No text annotation
J4_1FFK_008No text annotation
J4_1FFK_009No text annotation
J5_1FFK_001No text annotation
J5_1FFK_002No text annotation
J5_1FFK_003No text annotation
J5_1FFK_004No text annotation
J5_1FFK_005No text annotation
J5_1FFK_007No text annotation
J5_1FFK_008No text annotation
J6_1FFK_001No text annotation
J6_1FFK_002No text annotation
J7_1FFK_001No text annotation

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