Changes in PDB files used for clustering

Release 1.5 has 217 PDB files, release 1.6 has 217 PDB files, 216 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.6: 4KQY.

Obsolete: 3NPB4KQY.

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 1.5 has 249 motif groups, release 1.6 has 249 motif groups, 246 of them are identical.

3 motif groups were updated, 0 groups are present only in release 1.5, 0 groups are only in release 1.6.

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_72498.964T-loops with two bulged bases
2HL_39895.635UNCG Hairpin motifs
3HL_91226.317Kissing Hairpin motif
4HL_97270.315T-loops with 1 bulged base
5HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
6HL_49036.312GNRA with one bulged base
7HL_74465.212tRNA Anti-Codon loop
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_56824.210LSU Helix 60A. LSU Helix 63A.
12HL_27271.110LSU Helix 96 (H96) Hairpin Loop
13HL_68081.310LSU Helix 20 Hairpin loop
14HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
15HL_80459.39
16HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
17HL_15603.18U1A protein-binding Hairpin Loop.
18HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_34027.285S Loop C - Upper part of Hairpin Loop.
21HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
22HL_46489.26LSU H89 Hairpin Loop
23HL_39942.26LSU Helix 91 (H91) Hairpin Loop
24HL_57514.26Two base, cross-stacked hairpin loop
25HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
26HL_70420.26LSU Helix 97 Hairpin loop
27HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
28HL_18156.26LSU Helix 72 (H72) Hairpin Loop
29HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
30HL_42677.16
31HL_75579.26
32HL_87136.26LSU Helix 39A Hairpin loop
33HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
34HL_41833.26LSU Helix 81 (H81) Hairpin Loop
35HL_72273.15tRNA D-loop
36HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
37HL_45018.35Hairpin-Hairpin Interacting HL
38HL_06643.25tRNA D-loop. Sec tRNA
39HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
40HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
41HL_88311.25LSU Helix 35 (H35) Hairpin Loop
42HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
43HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
44HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
45HL_29831.14GNRA-like with bulged base.
46HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
47HL_11376.14LSU Helix 8 (H8) Hairpin Loop
48HL_98523.24GNRA-like. Closed by tSH UC.
49HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
50HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
51HL_47784.24SSU Central Pseudoknot (forms helix 2)
52HL_64543.24SSU Helix 31 (h31) Hairpin Loop
53HL_62881.14RNase P Structured Hairpin Loop
54HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
55HL_08382.23
56HL_42077.23LSU Helix 28 (H28) Hairpin Loop
57HL_23182.13
58HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
59HL_76766.23
60HL_68697.23
61HL_32644.13LSU Helix 69 (H69) Hairpin Loop
62HL_78361.13
63HL_21675.13LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
64HL_19221.23
65HL_13707.23cSH AA Platform containing Hairpin Loop
66HL_12595.23
67HL_76036.33LSU Helix 8 (H8) Hairpin Loop
68HL_42687.33
69HL_74686.13SSU Central Pseudoknot (forms helix 2)
70HL_90579.23
71HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
72HL_41827.13
73HL_58083.23
74HL_61547.43
75HL_80492.23tRNA D-loop
76HL_27429.33
77HL_25124.13tSW GA closed tetraloops
78HL_84353.12
79HL_42553.12
80HL_06312.12
81HL_64371.22
82HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
83HL_23129.12
84HL_91872.12
85HL_16770.12
86HL_33451.12
87HL_50312.12
88HL_26143.12
89HL_60200.12
90HL_24711.12
91HL_49210.12
92HL_94578.12
93HL_03791.12
94HL_74559.12Two base, cross-stacked hairpin loop
95HL_90542.12
96HL_91693.12
97HL_23290.12
98HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
99HL_19399.12
100HL_44467.12
101HL_18587.12
102HL_62967.12
103HL_81752.12
104HL_54751.22
105HL_24473.32tRNA D-loop
106HL_53753.12
107HL_17790.12UNCG-like. cWW Closing pair.
108HL_05361.12
109HL_98577.12
110HL_21545.12LSU Helix 96 (H96) Hairpin Loop
111HL_99633.12
112HL_93771.12tRNA T-loop distorted by RS binding
113HL_98833.22
114HL_38130.22
115HL_26495.12
116HL_96915.12
117HL_06997.12
118HL_06122.12
119HL_65924.12
120HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
121HL_75575.12
122HL_19528.12
123HL_87554.12
124HL_86398.12
125HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
126HL_33640.11
127HL_65802.11
128HL_35865.11
129HL_93633.11
130HL_57217.11cHS platform Intercalation Site
131HL_39422.11
132HL_66880.11
133HL_03785.11LSU Helix 8 (H8) Hairpin Loop
134HL_25175.11
135HL_90102.11Kink-turn-like Hairpin Loop
136HL_99207.11Tetrahymena LSU hairpin poorly modeled
137HL_17537.11
138HL_08203.11
139HL_55202.11U2B"-U2A" binding hairpin loop
140HL_56775.11
141HL_30128.11
142HL_48480.11
143HL_20806.11
144HL_52540.11
145HL_84289.11
146HL_27397.11
147HL_44390.11
148HL_67000.11
149HL_62970.11
150HL_93530.11
151HL_97784.11
152HL_85018.11
153HL_30008.11
154HL_38898.11
155HL_59610.11
156HL_77692.11tRNA D-loop
157HL_93567.11
158HL_99779.11
159HL_19226.11
160HL_95049.11Two base, cross-stacked hairpin loop
161HL_05113.11
162HL_34440.11
163HL_56809.11
164HL_62880.11
165HL_04194.11
166HL_95716.11
167HL_71607.11
168HL_19452.11tRNA D-loop
169HL_42345.11
170HL_17008.11Nova-2 KH3 domain binding hairpin
171HL_57923.11
172HL_78507.11
173HL_45358.11Double hairpin loop based on GGA triple
174HL_42969.11
175HL_79902.11
176HL_30731.11
177HL_07915.11
178HL_78228.11
179HL_97971.11
180HL_82243.11
181HL_10116.11Kink-turn-like Hairpin Loop
182HL_98233.11
183HL_96994.11
184HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
185HL_07315.11
186HL_45411.11
187HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
188HL_60203.11
189HL_68435.11
190HL_84888.11T-loop like but without tWH UA
191HL_57843.11
192HL_68579.11
193HL_27819.11
194HL_00090.11
195HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
196HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
197HL_75850.11
198HL_35200.11
199HL_69403.11GNRA-like
200HL_46570.11
201HL_73465.11
202HL_24108.11
203HL_73972.11
204HL_53789.11
205HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
206HL_87223.11
207HL_58223.11
208HL_19132.11
209HL_12706.11
210HL_67761.11
211HL_63304.11
212HL_39486.11
213HL_82288.11
214HL_83865.11
215HL_01418.11
216HL_59182.11
217HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
218HL_24707.11
219HL_25195.11
220HL_59604.11
221HL_97499.11
222HL_00721.11
223HL_26579.11
224HL_58601.11
225HL_88960.11
226HL_91613.11
227HL_70912.11
228HL_13786.11
229HL_55272.11
230HL_47337.11
231HL_33277.11
232HL_36842.11
233HL_23195.11
234HL_20028.11
235HL_38138.11
236HL_25197.11
237HL_37962.11
238HL_65071.11
239HL_44522.11
240HL_66877.11cSH GU/cWS double platform, intercalation site
241HL_53015.11
242HL_78420.11
243HL_68733.11LSU Yeast Hairpin Loop
244HL_66467.11
245HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
246HL_99584.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.9226GNRA Hairpin motifs
2HL_18781.420Double sheared (tSH) with U-turn
3HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription