6SE6

Class2 : CENP-A nucleosome in complex with CENP-C central region


Sequence Similarity Clusters for the Entities in PDB 6SE6

Entity #1 | Chains: A,E
Histone H3-like centromeric protein A protein, length: 140 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 8 11 3509
95 % 8 14 3182
90 % 9 16 2815
70 % 8 11 4460
50 % 221 299 73
40 % 221 299 96
30 % 221 299 95
Entity #2 | Chains: B,F
Histone H4 protein, length: 103 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 200 279 20
95 % 222 304 18
90 % 229 313 20
70 % 230 312 28
50 % 230 312 66
40 % 230 312 90
30 % 230 312 92
Entity #3 | Chains: C,G
Histone H2A type 2-A protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 6 9424
95 % 194 278 34
90 % 181 255 49
70 % 194 273 53
50 % 207 286 81
40 % 207 286 103
30 % 207 286 100
Entity #4 | Chains: D,H
Histone H2B type 1-C/E/F/G/I protein, length: 126 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 11 18 1669
95 % 153 189 80
90 % 197 274 43
70 % 205 285 49
50 % 210 292 76
40 % 210 292 99
30 % 210 292 98
Entity #5 | Chains: I
DNA (145-MER) dna, length: 145 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #6 | Chains: J
DNA (145-MER) dna, length: 145 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #7 | Chains: V
Centromere protein C protein, length: 124 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 3 37661
95 % 1 3 30006
90 % 1 3 28874
70 % 1 3 26087
50 % 1 3 22855
40 % 1 3 21265
30 % 1 3 19051

Instructions

In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff.



View more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB PDB.

You can also use the structure comparison tool to compare any 2 given structures


ACTION - (A) Select for download / view details OR (B) Select two chains for comparison
Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 1TZY 2 B, F Histone H2B 9031
2 1KX5 6 D, H histone H2B.2 8355
3 2ARO 2 B, F Histone H2B 9031
4 5B0Z 4 D, H Histone H2B type 1-J 9606
5 5Y0D 4 D, H Histone H2B type 1-J 9606
6 5Y0C 5 D, H Histone H2B type 1-J 9606
7 1S32 5 D, H Histone H2B 8355
8 5AV8 4 D, H Histone H2B type 1-J 9606
9 1KX3 5 D, H histone H2B.2 8355
10 5AV9 4 D, H Histone H2B type 1-J 9606
11 5AV6 4 D, H Histone H2B type 1-J 9606
12 6JOU 4 D, H Histone H2B type 1-J 9606
13 1HQ3 2 B, F HISTONE H2B 9031
14 3UTA 4 D, H Histone H2B 1.1 8355
15 6KVD 5 D, H Histone H2B type 1-J 9606
16 5X7X 4 D, H Histone H2B type 1-J 9606
17 5B31 4 D, H Histone H2B type 1-J 9606
18 5B1L 4 D, H Histone H2B type 3-A 10090
19 6K1K 4 D, H Histone H2B type 1-J 9606
20 3UTB 4 D, H Histone H2B 1.1 8355
21 1M19 5 D, H Histone H2B.1 8355
22 5AVB 4 D, H Histone H2B type 1-J 9606
23 5AVC 4 D, H Histone H2B type 1-J 9606
24 5AV5 4 D, H Histone H2B type 1-J 9606
25 3C1B 4 D, H Histone 2, H2bf 8364
26 5B1M 4 D, H Histone H2B type 3-A 10090
27 2NQB 5 D, H Histone H2B 7227
28 5OMX 6 D, H Histone H2B 1.1 8355
29 6JR1 4 D, H Histone H2B type 1-J 9606
30 5F99 4 D, H Histone H2B 1.1 8355
31 5Z30 4 D, H Histone H2B type 1-J 9606
32 5JRG 4 D, H Histone H2B type 1-J 9606
33 3UT9 4 D, H Histone H2B 1.1 8355
34 5B32 4 D, H Histone H2B type 1-J 9606
35 4WU8 6 D, H Histone H2B 1.1 8355
36 1P3I 5 D, H Histone H2B 8355
37 3MGR 4 D, H Histone H2B 1.1 8355
38 1F66 5 D, H HISTONE H2B 8355
39 3AZG 4 D, H Histone H2B type 1-J 9606
40 1M18 5 D, H Histone H2B.1 8355
41 5B2J 4 D, H Histone H2B type 1-J 9606
42 2PYO 6 D, H Histone H2B 7227
43 1P3L 5 D, H Histone H2B 8355
44 1EQZ 3 B, F PROTEIN (HISTONE H2B) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
45 5B0Y 4 D, H Histone H2B type 1-J 9606
46 6JR0 4 D, H Histone H2B type 1-J 9606
47 2CV5 5 D, H Histone H2B K 9606
48 5CP6 6 D, H Histone H2B 1.1 8355
49 5ZBX 4 D, H Histone H2B type 1-J 9606
50 5XF6 4 D, H Histone H2B 1.1 8355
51 3MGP 4 D, H Histone H2B 1.1 8355
52 3MVD 4 D, H Histone H2B 1.1 8355
53 4J8U 4 D, H Histone H2B 1.1 8355
54 4WU9 4 D, H Histone H2B 1.1 8355
55 3REH 4 D, H Histone H2B 1.1 8355
56 3AZL 4 D, H Histone H2B type 1-J 9606
57 5Z23 4 D, H Histone H2B type 1-J Se-Met-substituted H2B 9606
58 6N1Z 3 C, F Histone H2B 1.1 HISTONE H2B 1.1 8355
59 3AFA 4 D, H Histone H2B type 1-J 9606
60 5E5A 5 D, H Histone H2B 1.1 8355
61 3REJ 4 D, H Histone H2B 1.1 8355
62 3AZF 4 D, H Histone H2B type 1-J 9606
63 5GTC 4 D, H Histone H2B type 1-J 9606
64 1P3P 5 D, H Histone H2B 8355
65 3AV1 4 D, H Histone H2B type 1-J 9606
66 1M1A 5 D, H Histone H2B.1 8355
67 5CPK 4 D, H Histone H2B type 1-J 9606
68 5AY8 4 D, H Histone H2B type 1-J 9606
69 3MNN 4 D, H Histone H2B 1.1 8355
70 1P3G 5 D, H Histone H2B 8355
71 4J8W 4 D, H Histone H2B 1.1 8355
72 1P34 5 D, H Histone H2B 8355
73 5XF3 4 D, H Histone H2B type 1-J 9606
74 3X1V 5 D, H Histone H2B type 1-A 10090
75 5ONG 6 D, H Histone H2B 1.1 8355
76 5ONW 6 D, H Histone H2B 1.1 8355
77 5DNM 4 D, H Histone H2B 1.1 8355
78 6K1I 4 D, H Histone H2B type 1-J 9606
79 3MGQ 4 D, H Histone H2B 1.1 8355
80 3WTP 4 D, H Histone H2B type 1-J 9606
81 3X1T 5 D, H Histone H2B type 1-A 10090
82 2NZD 6 D, H Histone H2B 8355
83 3A6N 4 D, H Histone H2B type 1-J 9606
84 5DNN 4 D, H Histone H2B 1.1 8355
85 5GT3 4 D, H Histone H2B type 1-A 9606
86 5GT0 4 D, H Histone H2B type 1-J 9606
87 3LJA 4 D, H Histone H2B 1.1 8355
88 3AZI 4 D, H Histone H2B type 1-J 9606
89 3TU4 4 D, H Histone H2B 1.1 8355
90 1P3O 5 D, H Histone H2B 8355
91 1KX4 5 D, H histone H2B.2 8355
92 3AZN 4 D, H Histone H2B type 1-J 9606
93 1P3M 5 D, H Histone H2B 8355
94 4J8V 4 D, H Histone H2B 1.1 8355
95 5B33 4 D, H Histone H2B type 1-J 9606
96 3X1S 4 D, H Histone H2B type 1-B 9606
97 3LZ0 4 D, H Histone H2B 1.1 8355
98 1P3F 5 D, H Histone H2B 8355
99 1P3K 5 D, H Histone H2B 8355
100 5B2I 4 D, H Histone H2B type 1-J 9606
101 1P3A 5 D, H Histone H2B 8355
102 3LZ1 4 D, H Histone H2B 1.1 8355
103 5GXQ 4 D, H Histone H2B type 1-J 9606
104 2F8N 4 D Histone 3, H2ba 10090
105 2F8N 5 H Histone H2B.1 8355
106 4Z5T 4 D, H Histone H2B type 1-J 9606
107 1U35 5 D, H histone 3, H2ba 10090
108 5XM0 4 D, H Histone H2B type 3-A 10090
109 3AV2 4 D, H Histone H2B type 1-J 9606
110 3AYW 4 D, H Histone H2B type 1-J 9606
111 5XF5 4 D, H Histone H2B type 1-J 9606
112 3AZJ 4 D, H Histone H2B type 1-J 9606
113 3REK 4 D, H Histone H2B 1.1 8355
114 4KGC 4 D, H Histone H2B 1.1 8355
115 1ZLA 5 D, H histone H2B 8355
116 5GSU 4 D, H Histone H2B type 1-A 9606
117 5XF4 4 D, H Histone H2B type 1-J 9606
118 3REL 4 D, H Histone H2B 1.1 8355
119 5GSE 4 D, H, N Histone H2B type 1-J 9606
120 3REI 4 D, H Histone H2B 1.1 8355
121 1P3B 5 D, H Histone H2B 8355
122 3WKJ 4 D, H Histone H2B type 1-A 9606
123 3AZK 4 D, H Histone H2B type 1-J 9606
124 4J8X 4 D, H Histone H2B 1.1 8355
125 3LEL 4 D, H, N, R Histone H2B 1.1 8355
126 3KUY 4 D, H Histone H2B 8355
127 4R8P 4 D, H Histone H2B 1.1 8355
128 3AZM 4 D, H Histone H2B type 1-J 9606
129 3X1U 5 D, H Histone H2B type 1-B 9606
130 3MGS 4 D, H Histone H2B 1.1 8355
131 3WA9 4 D, H Histone H2B type 1-J 9606
132 3C1C 4 D, H Histone 2, H2bf 8364
133 3AZH 4 D, H Histone H2B type 1-J 9606
134 5B40 4 D, H Histone H2B type 1-J 9606
135 3WAA 4 D, H Histone H2B type 1-J 9606
136 5CPI 4 D, H Histone H2B type 1-J 9606
137 3W99 4 D, H Histone H2B type 1-J 9606
138 3AZE 4 D, H Histone H2B type 1-J 9606
139 3W96 4 D, H Histone H2B type 1-J 9606
140 6OM3 4 D, H, P, T Histone H2B 1.1 8355
141 5XM1 4 D, H Histone H2B type 3-A 10090
142 6K1J 4 D, H Histone H2B type 1-J 9606
143 5CPJ 4 D, H Histone H2B type 1-J 9606
144 5B24 4 D, H Histone H2B type 1-J 9606
145 2HIO 2 B PROTEIN (HISTONE H2B) 9031
146 4QLC 6 D, H Histone H2B 7227
147 4LD9 4 D, H Histone H2B 1.1 8355
148 3O62 4 D, H Histone H2B 1.1 8355
149 6KXV 4 D, H Histone H2B type 1-J 9606
150 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
151 4YM5 4 D, H Histone H2B type 1-J 9606
152 4YM6 4 D, H Histone H2B type 1-J 9606
153 2FJ7 6 D, H Histone H2B 8355
154 3W98 4 D, H Histone H2B type 1-J 9606
155 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
156 3AN2 4 D, H Histone H2B type 1-J 9606
157 6VYP 4 D, H, d, h Histone H2B 1.1 8355
158 3B6F 6 D, H Histone H2B 1.1 8355
159 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
160 3B6G 6 D, H Histone H2B 1.1 8355
161 5NL0 4 D, H, N Histone H2B 1.1 The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as a molecular replacement template (because it had the same 601L DNA sequence and therefore was the closest high-res structure available). 8355
162 3KXB 4 D, H Histone H2B 1.1 8355
163 5HQ2 4 H Histone H2B 1.1 8355
164 6HKT 4 1, 3, D, H, N, R, X, d, h, n, r, x Histone H2B type 1-J THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG 9606
165 5OXV 2 D, H, N, R Histone H2B 1.1 8355
166 1ZBB 6 D, H, d, h Histone H2B.1 8355
167 7JO9 4 D, H Histone H2B type 1-C/E/F/G/I 9606
168 7JOA 4 D, H Histone H2B type 1-C/E/F/G/I 9606
169 6XJD 4 D, H Histone H2B type 1-C/E/F/G/I 9606
170 6X59 4 D, H Histone H2B type 1-C/E/F/G/I 9606
171 6X5A 4 D, H Histone H2B type 1-C/E/F/G/I 9606
172 6X0N 4 D, H, d, h Histone H2B 1.1 8355
173 6WZ5 4 D, H Histone H2B 1.1 8355
174 6WZ9 4 D, H Histone H2B 1.1 8355
175 7C0M 4 D, H, d, h Histone H2B type 1-J 9606
176 6YOV 4 D, H Histone H2B type 1-J 9606
177 6LTJ 4 D, H Histone H2B 8355
178 6VEN 4 D, H Histone H2B 1.1 8355
179 6V92 26 d, h Histone H2B type 1-K 9606
180 6TEM 4 D, H Histone H2B 1.1 8355
181 6TDA 4 D, H Histone H2B 1.1 8355
182 6UXW 4 U, Y Histone H2B 1.1 RESIDUES 597-653 AND 765-780 OF CHAIN F, AND RESIDUES 609-655 AND 763-779 OF CHAIN G ARE NOT CONFIDENTLY ASSIGNED 8355
183 6T9L 4 D Histone H2B 1.1 8355
184 6T9L 5 H Histone H2B 8355
185 6T90 4 D, H Histone H2B type 1-J 9606
186 6T93 4 D, H Histone H2B type 1-J 9606
187 6T79 4 D, H Histone H2B type 1-K 9606
188 6T7A 4 D, H Histone H2B type 1-K 9606
189 6T7B 4 D, H Histone H2B type 1-K 9606
190 6T7C 4 D, H Histone H2B type 1-K 9606
191 6T7D 4 D, H Histone H2B type 1-K 9606
192 6UPK 4 D Histone H2B 9606
193 6UPL 4 D, L Histone H2B 9606
194 6L49 4 D, H, N, R, V, Z Histone H2B type 1-J 9606
195 6L4A 4 D, H, N, R, V, Z Histone H2B type 1-J 9606
196 6UGM 4 D Histone H2B 8355
197 6UGM 5 H Histone H2B 1.1 8355
198 6UH5 4 D Histone H2B 8355
199 6UH5 5 H Histone H2B 8355
200 6KW4 20 P, T Histone H4 8355
201 6KW5 18 U, Y Histone H4 8355
202 6KW3 20 P, T Histone H4 8355
203 6SEG 4 D, H Histone H2B type 1-C/E/F/G/I 9606
204 6SE0 4 D, H Histone H2B type 1-C/E/F/G/I 9606
205 6SE6 4 D, H Histone H2B type 1-C/E/F/G/I 9606
206 6SEE 4 D, H Histone H2B type 1-C/E/F/G/I 9606
207 6SEF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
208 6PX1 4 D, H Histone H2B 1.1 8355
209 6PX3 4 D, H Histone H2B 1.1 8355
210 6PWV 7 J, N Histone H2B 1.1 8355
211 6PWW 7 J, N Histone H2B 1.1 8355
212 6PWX 5 J, N Histone H2B 1.1 8355
213 6PWE 4 D, H Histone H2B 7227
214 6PWF 4 D, H Histone H2B 7227
215 6KIU 4 D, H Histone H2B 1.1 8355
216 6KIV 4 D, H Histone H2B 1.1 8355
217 6KIW 4 D, H Histone H2B 1.1 8355
218 6KIX 4 D, H Histone H2B 1.1 8355
219 6KIZ 4 D, H Histone H2B 1.1 8355
220 6S01 4 D, H Histone H2B 1.1 8355
221 6RYU 4 D, H Histone H2B 1.1 8355
222 6PA7 4 D, H Histone H2B 1.1 8355
223 6RYR 4 D, H Histone H2B 1.1 8355
224 6K1P 4 D, H Histone H2B 1.1 8355
225 6RNY 4 D, H Histone H2B type 1-C/E/F/G/I 9606
226 6JYL 4 D, H Histone H2B 1.1 8355
227 6R8Y 4 D, H Histone H2B type 1-J 9606
228 6R8Z 4 D, H Histone H2B type 1-J 9606
229 6R90 4 D, H Histone H2B type 1-J 9606
230 6R91 4 D, H Histone H2B type 1-J 9606
231 6R92 7 D, H Histone H2B type 1-J 9606
232 6R93 6 D, H Histone H2B type 1-J 9606
233 6R94 6 D, H Histone H2B type 1-J 9606
234 6R1U 4 D, H Histone H2B 1.1 8355
235 6R25 7 D, H H2B 8355
236 6O96 4 D, H Histone H2B 1.1 8355
237 6R0C 4 D, H Histone H2B type 1-C/E/F/G/I 9606
238 6O1D 4 D, H Histone H2B type 1-J 9606
239 6NZO 4 D, H Histone H2B 1.1 8355
240 6J99 4 D, H Histone H2B 1.1 8355
241 6NQA 5 D, H Histone H2B 1.1 8355
242 6NOG 4 D, H Histone H2B 1.1 8355
243 6NN6 4 D, H Histone H2B 1.1 8355
244 6J4W 22 d, h Histone H2B type 1-J 9606
245 6J4X 22 d, h Histone H2B type 1-J 9606
246 6J4Y 22 d, h Histone H2B type 1-J 9606
247 6J4Z 21 d, h Histone H2B type 1-J 9606
248 6J50 21 d, h Histone H2B type 1-J 9606
249 6J51 22 d, h Histone H2B type 1-J 9606
250 6NJ9 3 D, H Histone H2B 1.1 8355
251 6I84 6 R, W Histone H2B 1.1 8355
252 6IRO 5 D, H Histone H2B 1.1 8355
253 6IR9 22 d, h Histone H2B type 1-J 9606
254 6INQ 19 d, h Histone H2B type 1-J 9606
255 6HTS 8 L, P Histone H2B type 1-J 9606
256 6E0C 4 D, H Histone H2B type 1-J 9606
257 6E0P 4 D, H Histone H2B type 1-J 9606
258 6DZT 4 D, H Histone H2B 7227
259 6A5O 19 d, h Histone H2B type 1-J 9606
260 6A5P 19 d, h Histone H2B type 1-J 9606
261 6A5R 19 d, h Histone H2B type 1-J 9606
262 6A5T 19 d, h Histone H2B type 1-J 9606
263 6A5U 19 d, h Histone H2B, Histone H2B type 1-J 9606
264 6A5L 19 d, h Histone H2B type 1-J 9606
265 6G0L 4 D, H Histone H4 8355
266 6FTX 4 D, H Histone H2B 8364
267 6FML 12 P, T Histone H2B type 1-C/E/F/G/I 9606
268 5Z3L 4 D, H Histone H2B 1.1 8355
269 5Z3O 4 D, H Histone H2B 1.1 8355
270 5Z3U 5 D, H Histone H2B 1.1 8355
271 5Z3V 5 D, H Histone H2B 1.1 8355
272 6C0W 4 D, H Histone H2B 9606
273 6BUZ 4 D, H Histone H2B 9606
274 6ESF 4 D, H Histone H2B 1.1 8355
275 6ESG 4 D, H Histone H2B 1.1 8355
276 6ESH 4 D, H Histone H2B 1.1 8355
277 6ESI 4 D Histone H2B 1.1 8355
278 6ESI 5 H Histone H2B 1.1 8355
279 5O9G 4 D Histone H2B 1.1 8355
280 5O9G 5 H Histone H2B 1.1 8355
281 5X0X 4 D, H Histone H2B 1.1 8355
282 5X0Y 4 D, H Histone H2B 1.1 8355
283 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
284 2RVQ 2 D Histone H2B type 1-J 9606
285 3C9K 2 B, F Histone H2B 7 9031