Changes in PDB files used for clustering

Release 1.4 has 211 PDB files, release 1.5 has 212 PDB files, 209 of them are identical.

1 equivalence classes changed representatives: 2XZM4BPP.

2 new structures in release 1.5: 4L8R, 4LCK.

Obsolete: 2XZM4V5O, 4HXH4L8R.

Help Every Motif Atlas release is based on a representative set of PDB files. When comparing two releases, it's important to know how the input data changed.

Representative sets are quite stable in time, but PDB files from the older releases can be replaced by newer PDB files or removed from the set altogether if the structure is obsoleted by PDB without replacement.

PDB files from the newer release either replace representatives in the existing equivalence classes or come from new equivalence classes.

Redistribution of motif instances

Loading the Sankey diagram...

Changes in motif groups

Release 1.4 has 256 motif groups, release 1.5 has 249 motif groups, 193 of them are identical.

27 motif groups were updated, 36 groups are present only in release 1.4, 29 groups are only in release 1.5.

Help The Sankey diagram shows redistribution of motif instances (loops) between two releases. The rectangles represent the motif groups and are colored as follows:

Added motif groups: green
Removed motif groups: grey
Updated motif groups: orange
Added motif instances: green
Removed motif instances: grey

Hover over the links connecting the motif groups to see which motif instances were exchanged.


Identical motif groups

#Motif idInstancesDescription
1HL_91226.317Kissing Hairpin motif
2HL_74465.212tRNA Anti-Codon loop
3HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
4HL_56824.210LSU Helix 60A. LSU Helix 63A.
5HL_68081.310LSU Helix 20 Hairpin loop
6HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
7HL_34027.285S Loop C - Upper part of Hairpin Loop.
8HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
9HL_15603.18U1A protein-binding Hairpin Loop.
10HL_41833.26LSU Helix 81 (H81) Hairpin Loop
11HL_70420.26LSU Helix 97 Hairpin loop
12HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
13HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
14HL_75579.26
15HL_18156.26LSU Helix 72 (H72) Hairpin Loop
16HL_46489.26LSU H89 Hairpin Loop
17HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
18HL_42677.16
19HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
20HL_39942.26LSU Helix 91 (H91) Hairpin Loop
21HL_87136.26LSU Helix 39A Hairpin loop
22HL_45018.35Hairpin-Hairpin Interacting HL
23HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
24HL_88311.25LSU Helix 35 (H35) Hairpin Loop
25HL_06643.25tRNA D-loop. Sec tRNA
26HL_72273.15tRNA D-loop
27HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
28HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
29HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
30HL_29831.14GNRA-like with bulged base.
31HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
32HL_62881.14RNase P Structured Hairpin Loop
33HL_25124.13tSW GA closed tetraloops
34HL_74686.13SSU Central Pseudoknot (forms helix 2)
35HL_42077.23LSU Helix 28 (H28) Hairpin Loop
36HL_23182.13
37HL_76036.33LSU Helix 8 (H8) Hairpin Loop
38HL_80492.23tRNA D-loop
39HL_13707.23cSH AA Platform containing Hairpin Loop
40HL_19221.23
41HL_32644.13LSU Helix 69 (H69) Hairpin Loop
42HL_90579.23
43HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
44HL_58083.23
45HL_08382.23
46HL_27429.33
47HL_41827.13
48HL_78361.13
49HL_16770.12
50HL_38130.22
51HL_49210.12
52HL_62967.12
53HL_87554.12
54HL_05361.12
55HL_75575.12
56HL_84353.12
57HL_94578.12
58HL_06122.12
59HL_98577.12
60HL_06312.12
61HL_23290.12
62HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
63HL_50312.12
64HL_64371.22
65HL_26495.12
66HL_42553.12
67HL_60200.12
68HL_99633.12
69HL_24473.32tRNA D-loop
70HL_53753.12
71HL_81752.12
72HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
73HL_96915.12
74HL_65924.12
75HL_03791.12
76HL_19399.12
77HL_24711.12
78HL_33451.12
79HL_04194.11
80HL_10116.11Kink-turn-like Hairpin Loop
81HL_19452.11tRNA D-loop
82HL_27819.11
83HL_33640.11
84HL_44522.11
85HL_55272.11
86HL_58601.11
87HL_66467.11
88HL_69403.11GNRA-like
89HL_78420.11
90HL_84289.11
91HL_93567.11
92HL_97784.11
93HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
94HL_17537.11
95HL_20806.11
96HL_25175.11
97HL_38138.11
98HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
99HL_56775.11
100HL_59182.11
101HL_62970.11
102HL_66877.11cSH GU/cWS double platform, intercalation site
103HL_78507.11
104HL_97971.11
105HL_25195.11
106HL_30008.11
107HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
108HL_42345.11
109HL_45411.11
110HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
111HL_56809.11
112HL_59604.11
113HL_63304.11
114HL_67000.11
115HL_70912.11
116HL_84888.11T-loop like but without tWH UA
117HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
118HL_25197.11
119HL_30128.11
120HL_34440.11
121HL_39422.11
122HL_59610.11
123HL_67761.11
124HL_71607.11
125HL_75850.11
126HL_79902.11
127HL_85018.11
128HL_88960.11
129HL_95049.11Two base, cross-stacked hairpin loop
130HL_99207.11Tetrahymena LSU hairpin poorly modeled
131HL_00090.11
132HL_12706.11
133HL_19132.11
134HL_24108.11
135HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
136HL_35200.11
137HL_39486.11
138HL_47337.11
139HL_53015.11
140HL_57217.11cHS platform Intercalation Site
141HL_65071.11
142HL_90102.11Kink-turn-like Hairpin Loop
143HL_95716.11
144HL_01418.11
145HL_07315.11
146HL_26579.11
147HL_35865.11
148HL_57843.11
149HL_60203.11
150HL_65802.11
151HL_68435.11
152HL_77692.11tRNA D-loop
153HL_07915.11
154HL_13786.11
155HL_19226.11
156HL_24707.11
157HL_27397.11
158HL_33277.11
159HL_36842.11
160HL_42969.11
161HL_53789.11
162HL_62880.11
163HL_68579.11
164HL_73465.11
165HL_78228.11
166HL_82243.11
167HL_96994.11
168HL_37962.11
169HL_44390.11
170HL_48480.11
171HL_55202.11U2B"-U2A" binding hairpin loop
172HL_58223.11
173HL_68733.11LSU Yeast Hairpin Loop
174HL_82288.11
175HL_87223.11
176HL_93530.11
177HL_97499.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.8226GNRA Hairpin motifs
2HL_72498.964T-loops with two bulged bases
3HL_39895.635UNCG Hairpin motifs
4HL_18781.320Double sheared (tSH) with U-turn
5HL_97270.315T-loops with 1 bulged base
6HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_49036.312GNRA with one bulged base
8HL_48039.211MS2 virus RNA Hairpin
9HL_46175.21016S helix 23 and 24 hairpin loops
10HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
11HL_80459.39
12HL_82294.38SSU Helix 37 (h37) Hairpin loop.
13HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
14HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
15HL_57514.26Two base, cross-stacked hairpin loop
16HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
17HL_47784.24SSU Central Pseudoknot (forms helix 2)
18HL_64543.24SSU Helix 31 (h31) Hairpin Loop
19HL_98523.24GNRA-like. Closed by tSH UC.
20HL_12595.23
21HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
22HL_68697.23
23HL_76766.23
24HL_42687.33
25HL_61547.43
26HL_98833.22
27HL_54751.22

Removed motif groups

#Motif idInstancesDescription
1HL_28436.39LSU Helix 96 (H96) Hairpin Loop
2HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
3HL_77235.34LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
4HL_18798.14UNCG-like. cWW Closing pair.
5HL_46794.23
6HL_82253.23
7HL_26057.12
8HL_67367.12
9HL_67692.12
10HL_57014.12
11HL_77555.12
12HL_97512.12LSU Helix 8 (H8) Hairpin Loop
13HL_57904.12
14HL_58687.12
15HL_45440.12
16HL_66900.11
17HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
18HL_52109.11
19HL_85753.11
20HL_12984.11
21HL_29084.11
22HL_52393.11Double tSH (double sheared) with bulged base
23HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
24HL_13105.11
25HL_31969.11
26HL_55543.11
27HL_96192.11
28HL_16118.11
29HL_33524.11tRNA T-loop distorted by RS binding
30HL_17468.11
31HL_34375.11
32HL_80746.11
33HL_35004.11
34HL_81295.11UNCG-like. cWW Closing pair.
35HL_20914.11
36HL_63690.11

Added motif groups

#Motif idInstancesDescription
1HL_27271.110LSU Helix 96 (H96) Hairpin Loop
2HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
3HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
4HL_11376.14LSU Helix 8 (H8) Hairpin Loop
5HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
6HL_21675.13LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
8HL_90542.12
9HL_23129.12
10HL_91693.12
11HL_06997.12
12HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
13HL_91872.12
14HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
15HL_17790.12UNCG-like. cWW Closing pair.
16HL_26143.12
17HL_93771.12tRNA T-loop distorted by RS binding
18HL_18587.12
19HL_74559.12Two base, cross-stacked hairpin loop
20HL_19528.12
21HL_21545.12LSU Helix 96 (H96) Hairpin Loop
22HL_86398.12
23HL_52540.11
24HL_03785.11LSU Helix 8 (H8) Hairpin Loop
25HL_23195.11
26HL_93633.11
27HL_73972.11
28HL_83865.11
29HL_46570.11
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