Changes in PDB files used for clustering

Release 1.5 has 212 PDB files, release 1.6 has 212 PDB files, 211 of them are identical.

1 equivalence classes changed representatives: 3NPB4KQY.

No new PDB files have been added.

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_74465.212tRNA Anti-Codon loop
7HL_49036.312GNRA with one bulged base
8HL_48039.211MS2 virus RNA Hairpin
9HL_68081.310LSU Helix 20 Hairpin loop
10HL_46175.21016S helix 23 and 24 hairpin loops
11HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
12HL_56824.210LSU Helix 60A. LSU Helix 63A.
13HL_27271.110LSU Helix 96 (H96) Hairpin Loop
14HL_80459.39
15HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16HL_15603.18U1A protein-binding Hairpin Loop.
17HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18HL_82294.38SSU Helix 37 (h37) Hairpin loop.
19HL_34027.285S Loop C - Upper part of Hairpin Loop.
20HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
23HL_70420.26LSU Helix 97 Hairpin loop
24HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
25HL_18156.26LSU Helix 72 (H72) Hairpin Loop
26HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
27HL_42677.16
28HL_75579.26
29HL_87136.26LSU Helix 39A Hairpin loop
30HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
31HL_41833.26LSU Helix 81 (H81) Hairpin Loop
32HL_57514.26Two base, cross-stacked hairpin loop
33HL_46489.26LSU H89 Hairpin Loop
34HL_39942.26LSU Helix 91 (H91) Hairpin Loop
35HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
36HL_06643.25tRNA D-loop. Sec tRNA
37HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
38HL_72273.15tRNA D-loop
39HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
40HL_45018.35Hairpin-Hairpin Interacting HL
41HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
42HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
43HL_88311.25LSU Helix 35 (H35) Hairpin Loop
44HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
45HL_62881.14RNase P Structured Hairpin Loop
46HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
47HL_29831.14GNRA-like with bulged base.
48HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
49HL_11376.14LSU Helix 8 (H8) Hairpin Loop
50HL_98523.24GNRA-like. Closed by tSH UC.
51HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
52HL_47784.24SSU Central Pseudoknot (forms helix 2)
53HL_64543.24SSU Helix 31 (h31) Hairpin Loop
54HL_13707.23cSH AA Platform containing Hairpin Loop
55HL_12595.23
56HL_74686.13SSU Central Pseudoknot (forms helix 2)
57HL_27429.33
58HL_76766.23
59HL_78361.13
60HL_42687.33
61HL_41827.13
62HL_58083.23
63HL_80492.23tRNA D-loop
64HL_68697.23
65HL_61547.43
66HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
67HL_32644.13LSU Helix 69 (H69) Hairpin Loop
68HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
69HL_08382.23
70HL_42077.23LSU Helix 28 (H28) Hairpin Loop
71HL_23182.13
72HL_76036.33LSU Helix 8 (H8) Hairpin Loop
73HL_25124.13tSW GA closed tetraloops
74HL_90579.23
75HL_21675.13LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
76HL_19221.23
77HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
78HL_81752.12
79HL_54751.22
80HL_24473.32tRNA D-loop
81HL_96915.12
82HL_53753.12
83HL_17790.12UNCG-like. cWW Closing pair.
84HL_26495.12
85HL_06312.12
86HL_21545.12LSU Helix 96 (H96) Hairpin Loop
87HL_86398.12
88HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
89HL_93771.12tRNA T-loop distorted by RS binding
90HL_98833.22
91HL_38130.22
92HL_42553.12
93HL_50312.12
94HL_19528.12
95HL_87554.12
96HL_91872.12
97HL_06122.12
98HL_65924.12
99HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
100HL_75575.12
101HL_33451.12
102HL_98577.12
103HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
104HL_23129.12
105HL_26143.12
106HL_60200.12
107HL_84353.12
108HL_19399.12
109HL_74559.12Two base, cross-stacked hairpin loop
110HL_90542.12
111HL_06997.12
112HL_16770.12
113HL_94578.12
114HL_03791.12
115HL_18587.12
116HL_62967.12
117HL_24711.12
118HL_49210.12
119HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
120HL_64371.22
121HL_91693.12
122HL_23290.12
123HL_05361.12
124HL_99633.12
125HL_53789.11
126HL_25195.11
127HL_37962.11
128HL_68579.11
129HL_12706.11
130HL_13786.11
131HL_55272.11
132HL_47337.11
133HL_33277.11
134HL_36842.11
135HL_23195.11
136HL_42345.11
137HL_73972.11
138HL_24707.11
139HL_57217.11cHS platform Intercalation Site
140HL_52540.11
141HL_42969.11
142HL_79902.11
143HL_70912.11
144HL_53015.11
145HL_78420.11
146HL_68733.11LSU Yeast Hairpin Loop
147HL_66467.11
148HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
149HL_96994.11
150HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
151HL_25197.11
152HL_20806.11
153HL_95049.11Two base, cross-stacked hairpin loop
154HL_84888.11T-loop like but without tWH UA
155HL_57843.11
156HL_03785.11LSU Helix 8 (H8) Hairpin Loop
157HL_25175.11
158HL_90102.11Kink-turn-like Hairpin Loop
159HL_99207.11Tetrahymena LSU hairpin poorly modeled
160HL_17537.11
161HL_24108.11
162HL_38138.11
163HL_93633.11
164HL_19226.11
165HL_68435.11
166HL_19132.11
167HL_62970.11
168HL_93530.11
169HL_97784.11
170HL_85018.11
171HL_59182.11
172HL_33640.11
173HL_65802.11
174HL_35865.11
175HL_30128.11
176HL_48480.11
177HL_78507.11
178HL_58223.11
179HL_58601.11
180HL_88960.11
181HL_44390.11
182HL_67000.11
183HL_62880.11
184HL_04194.11
185HL_95716.11
186HL_71607.11
187HL_19452.11tRNA D-loop
188HL_56775.11
189HL_93567.11
190HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
191HL_60203.11
192HL_26579.11
193HL_66877.11cSH GU/cWS double platform, intercalation site
194HL_56809.11
195HL_78228.11
196HL_97971.11
197HL_82243.11
198HL_10116.11Kink-turn-like Hairpin Loop
199HL_73465.11
200HL_59610.11
201HL_77692.11tRNA D-loop
202HL_45411.11
203HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
204HL_87223.11
205HL_44522.11
206HL_27397.11
207HL_07915.11
208HL_00090.11
209HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
210HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
211HL_75850.11
212HL_35200.11
213HL_69403.11GNRA-like
214HL_46570.11
215HL_01418.11
216HL_55202.11U2B"-U2A" binding hairpin loop
217HL_07315.11
218HL_59604.11
219HL_97499.11
220HL_65071.11
221HL_39422.11
222HL_84289.11
223HL_34440.11
224HL_27819.11
225HL_67761.11
226HL_63304.11
227HL_39486.11
228HL_82288.11
229HL_83865.11
230HL_30008.11

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