RNA 3D Hub //

7PKQ Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7PKQ_0011/1/10:20No text annotation
geometric
HL_4V88_186
NA
HL_7PKQ_0031/2/17:23No text annotation
geometric
HL_8G9Z_001
HL_75660.8
HL_7PKQ_0041/2/64:79Mini UNCG
geometric
HL_4YAZ_004
HL_90436.3
HL_7PKQ_0231/2/106:111GNRA
geometric
HL_1KXK_001
NA
HL_7PKQ_0061/2/129:141No text annotation
HL_7PKQ_0081/2/187:193No text annotation
geometric
HL_2Y9H_003
HL_75660.8
HL_7PKQ_0091/3/34:39No text annotation
geometric
HL_1WZ2_007
HL_75660.8
HL_7PKQ_0101/3/142:151No text annotation
homologous
HL_6CZR_086
NA
HL_7PKQ_0111/3/179:184GNRA
homologous
HL_4LFB_016
HL_34789.4
HL_7PKQ_0121/3/238:248No text annotation
geometric
HL_5ID6_001
HL_69752.4
HL_7PKQ_0131/3/278:289No text annotation
HL_7PKQ_0141/3/311:316GNRA
homologous
HL_6CZR_091
NA
HL_7PKQ_0251/4/356:369No text annotation

Problematic loops

#loop idProblemSequence
HL_7PKQ_002No text annotation
HL_7PKQ_005tRNA anticodon loop
HL_7PKQ_007UNCG
HL_7PKQ_015No text annotation
HL_7PKQ_024No text annotation
HL_7PKQ_016No text annotation
HL_7PKQ_017No text annotation
HL_7PKQ_018No text annotation
HL_7PKQ_019T-loop with 2 stacked bulged bases
HL_7PKQ_020No text annotation
HL_7PKQ_021No text annotation
HL_7PKQ_022GNRA

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7PKQ_0631/1/29:31,
1/3/63:64		Single bulged C
geometric
IL_3D0U_001
IL_05642.3
IL_7PKQ_0641/2/8:10,
1/2/29:31		No text annotation
geometric
IL_8P9A_384
IL_87720.1
IL_7PKQ_0051/2/13:15,
1/2/25:26		Single bulged A
geometric
IL_4V88_409
NA
IL_7PKQ_0491/2/13:16,
1/2/24:26		Decoding loop related
geometric
IL_2O3X_003
IL_53541.1
IL_7PKQ_0061/2/47:52,
1/2/89:94		No text annotation
IL_7PKQ_0651/2/53:59,
1/2/84:88		No text annotation
IL_7PKQ_0081/2/100:105,
1/2/112:119		No text annotation
IL_7PKQ_0091/2/175:177,
1/2/201:202		Single bulged U
geometric
IL_4LFB_014
IL_97561.5
IL_7PKQ_0101/2/179:183,
1/2/198:199		C-loop
geometric
IL_4LFB_015
IL_26900.1
IL_7PKQ_0111/2/183:184,
1/2/196:198		Single bulged G
geometric
IL_5J7L_019
NA
IL_7PKQ_0121/3/16:23,
1/3/52:53		SSU/LSU pseudoknot
homologous
IL_5J7L_024
NA
IL_7PKQ_0131/3/27:33,
1/3/40:48		Kink-turn related
geometric
IL_6CZR_133
NA
IL_7PKQ_0141/3/81:87,
1/3/295:296		No text annotation
homologous
IL_5J7L_026
NA
IL_7PKQ_0521/3/91:97,
1/3/208:214		No text annotation
IL_7PKQ_0151/3/92:97,
1/3/208:213		No text annotation
IL_7PKQ_0161/3/98:107,
1/3/206:207		No text annotation
IL_7PKQ_0531/3/98:108,
1/3/203:207		No text annotation
IL_7PKQ_0541/3/107:108,
1/3/203:206		Major groove platform; stack outside cWW
geometric
IL_4WF9_049
IL_74641.2
IL_7PKQ_0551/3/108:112,
1/3/199:203		Partly complementary
geometric
IL_7VYX_008
IL_71154.3
IL_7PKQ_0181/3/116:119,
1/3/193:195		Decoding loop related
geometric
IL_5Z1I_002
NA
IL_7PKQ_0191/3/119:121,
1/3/191:193		Isolated non-canonical cWW pair
geometric
IL_6IA2_004
IL_01003.4
IL_7PKQ_0201/3/127:131,
1/3/165:169		Triple non-canonical cWW pairs
homologous
IL_5J7L_361
NA
IL_7PKQ_0581/3/226:230,
1/3/256:258		No text annotation
IL_7PKQ_0231/3/231:235,
1/3/251:255		tSH-tHW-tHS
homologous
IL_5J7L_037
NA
IL_7PKQ_0261/3/336:337,
1/4/304:306		Single bulged A
homologous
IL_5J7L_039
NA
IL_7PKQ_0591/3/336:338,
1/4/303:306		Other IL
geometric
IL_5M0H_001
NA

Problematic loops

#loop idProblemSequence
IL_7PKQ_001Isolated non-canonical cWW pair
IL_7PKQ_002Isolated non-canonical cWW pair
IL_7PKQ_003Minor groove platform
IL_7PKQ_004Tandem non-canonical cWW pairs
IL_7PKQ_050No text annotation
IL_7PKQ_007No text annotation
IL_7PKQ_051No text annotation
IL_7PKQ_017No text annotation
IL_7PKQ_056No text annotation
IL_7PKQ_021Kink-turn
IL_7PKQ_057Single stack bend
IL_7PKQ_022No text annotation
IL_7PKQ_024Isolated cWS basepair
IL_7PKQ_025No text annotation
IL_7PKQ_027No text annotation
IL_7PKQ_060Single bulged G
IL_7PKQ_028Isolated non-canonical cWW pair
IL_7PKQ_029No text annotation
IL_7PKQ_030Single bulged U
IL_7PKQ_031Isolated cWS basepair
IL_7PKQ_061No text annotation
IL_7PKQ_032Minor groove platform with extra cWW
IL_7PKQ_033Single bulged U
IL_7PKQ_062No text annotation
IL_7PKQ_034No text annotation
IL_7PKQ_035Isolated non-canonical cWW pair
IL_7PKQ_036No text annotation
IL_7PKQ_037Isolated cWS basepair
IL_7PKQ_038Isolated non-canonical cWW pair
IL_7PKQ_039No text annotation
IL_7PKQ_040Isolated non-canonical cWW pair
IL_7PKQ_041Double sheared with near cWW
IL_7PKQ_042No text annotation
IL_7PKQ_043Isolated cWH basepair
IL_7PKQ_044Isolated non-canonical cWW pair
IL_7PKQ_045UAA/GAN with extra stack
IL_7PKQ_046Double sheared
IL_7PKQ_047No text annotation
IL_7PKQ_048Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7PKQ_0081/1/45:53,
1/2/167:175,
1/2/202:205		No text annotation
J3_7PKQ_0011/3/125:127,
1/3/169:178,
1/3/185:187		No text annotation
J4_7PKQ_0041/1/34:39,
1/2/211:213,
1/3/5:12,
1/3/57:60		No text annotation
J4_7PKQ_0051/1/84:92,
1/2/43:45,
1/2/96:99,
1/2/120:121		No text annotation
J4_7PKQ_0031/3/87:89,
1/3/216:221,
1/3/262:273,
1/3/294:295		No text annotation
homologous
J4_6CZR_013
NA
J5_7PKQ_0011/1/59:62,
1/1/76:82,
1/2/123:125,
1/2/145:146,
1/2/159:162		No text annotation

Problematic loops

#loop idProblemSequence
J3_7PKQ_005No text annotation
J3_7PKQ_006No text annotation
J3_7PKQ_009No text annotation
J3_7PKQ_002No text annotation
J3_7PKQ_003No text annotation
J3_7PKQ_004No text annotation
J3_7PKQ_007No text annotation
J4_7PKQ_001No text annotation
J4_7PKQ_002No text annotation

Coloring options:
Copyright 2026 BGSU RNA group. Page generated in 0.0527 s