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 3842
95 % 8 14 3307
90 % 9 16 2922
70 % 8 11 4641
50 % 241 319 63
40 % 241 319 83
30 % 241 319 91
Entity #2 | Chains: B,F
Histone H4 protein, length: 103 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 221 300 9
95 % 243 325 17
90 % 250 334 18
70 % 251 333 25
50 % 251 333 58
40 % 251 333 77
30 % 251 333 81
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 % 5 7 6122
95 % 216 300 18
90 % 199 273 44
70 % 212 291 38
50 % 225 304 69
40 % 225 304 88
30 % 225 304 97
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 % 12 19 1605
95 % 169 205 75
90 % 218 295 25
70 % 226 306 31
50 % 231 313 67
40 % 231 313 86
30 % 231 313 94
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 36825
95 % 1 3 30394
90 % 1 3 29239
70 % 1 3 26344
50 % 1 3 25020
40 % 1 3 22794
30 % 1 3 18885

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 6V2K 4 D, H Histone H2B type 1-J 9606
43 2PYO 6 D, H Histone H2B 7227
44 1P3L 5 D, H Histone H2B 8355
45 1EQZ 3 B, F PROTEIN (HISTONE H2B) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
46 5B0Y 4 D, H Histone H2B type 1-J 9606
47 6JR0 4 D, H Histone H2B type 1-J 9606
48 2CV5 5 D, H Histone H2B K 9606
49 5CP6 6 D, H Histone H2B 1.1 8355
50 5ZBX 4 D, H Histone H2B type 1-J 9606
51 5XF6 4 D, H Histone H2B 1.1 8355
52 3MGP 4 D, H Histone H2B 1.1 8355
53 3MVD 4 D, H Histone H2B 1.1 8355
54 4J8U 4 D, H Histone H2B 1.1 8355
55 4WU9 4 D, H Histone H2B 1.1 8355
56 3REH 4 D, H Histone H2B 1.1 8355
57 3AZL 4 D, H Histone H2B type 1-J 9606
58 5Z23 4 D, H Histone H2B type 1-J Se-Met-substituted H2B 9606
59 6N1Z 3 C, F Histone H2B 1.1 HISTONE H2B 1.1 8355
60 3AFA 4 D, H Histone H2B type 1-J 9606
61 5E5A 5 D, H Histone H2B 1.1 8355
62 3REJ 4 D, H Histone H2B 1.1 8355
63 3AZF 4 D, H Histone H2B type 1-J 9606
64 5GTC 4 D, H Histone H2B type 1-J 9606
65 1P3P 5 D, H Histone H2B 8355
66 3AV1 4 D, H Histone H2B type 1-J 9606
67 1M1A 5 D, H Histone H2B.1 8355
68 5CPK 4 D, H Histone H2B type 1-J 9606
69 5AY8 4 D, H Histone H2B type 1-J 9606
70 3MNN 4 D, H Histone H2B 1.1 8355
71 1P3G 5 D, H Histone H2B 8355
72 4J8W 4 D, H Histone H2B 1.1 8355
73 1P34 5 D, H Histone H2B 8355
74 5XF3 4 D, H Histone H2B type 1-J 9606
75 3X1V 5 D, H Histone H2B type 1-A 10090
76 5ONG 6 D, H Histone H2B 1.1 8355
77 5ONW 6 D, H Histone H2B 1.1 8355
78 5DNM 4 D, H Histone H2B 1.1 8355
79 6K1I 4 D, H Histone H2B type 1-J 9606
80 3MGQ 4 D, H Histone H2B 1.1 8355
81 3WTP 4 D, H Histone H2B type 1-J 9606
82 3X1T 5 D, H Histone H2B type 1-A 10090
83 2NZD 6 D, H Histone H2B 8355
84 3A6N 4 D, H Histone H2B type 1-J 9606
85 5DNN 4 D, H Histone H2B 1.1 8355
86 5GT3 4 D, H Histone H2B type 1-A 9606
87 5GT0 4 D, H Histone H2B type 1-J 9606
88 3LJA 4 D, H Histone H2B 1.1 8355
89 3AZI 4 D, H Histone H2B type 1-J 9606
90 3TU4 4 D, H Histone H2B 1.1 8355
91 1P3O 5 D, H Histone H2B 8355
92 1KX4 5 D, H histone H2B.2 8355
93 3AZN 4 D, H Histone H2B type 1-J 9606
94 1P3M 5 D, H Histone H2B 8355
95 4J8V 4 D, H Histone H2B 1.1 8355
96 5B33 4 D, H Histone H2B type 1-J 9606
97 3X1S 4 D, H Histone H2B type 1-B 9606
98 3LZ0 4 D, H Histone H2B 1.1 8355
99 1P3F 5 D, H Histone H2B 8355
100 1P3K 5 D, H Histone H2B 8355
101 5B2I 4 D, H Histone H2B type 1-J 9606
102 1P3A 5 D, H Histone H2B 8355
103 3LZ1 4 D, H Histone H2B 1.1 8355
104 5GXQ 4 D, H Histone H2B type 1-J 9606
105 2F8N 4 D Histone 3, H2ba 10090
106 2F8N 5 H Histone H2B.1 8355
107 4Z5T 4 D, H Histone H2B type 1-J 9606
108 1U35 5 D, H histone 3, H2ba 10090
109 5XM0 4 D, H Histone H2B type 3-A 10090
110 3AV2 4 D, H Histone H2B type 1-J 9606
111 3AYW 4 D, H Histone H2B type 1-J 9606
112 5XF5 4 D, H Histone H2B type 1-J 9606
113 3AZJ 4 D, H Histone H2B type 1-J 9606
114 3REK 4 D, H Histone H2B 1.1 8355
115 4KGC 4 D, H Histone H2B 1.1 8355
116 1ZLA 5 D, H histone H2B 8355
117 5GSU 4 D, H Histone H2B type 1-A 9606
118 5XF4 4 D, H Histone H2B type 1-J 9606
119 3REL 4 D, H Histone H2B 1.1 8355
120 5GSE 4 D, H, N Histone H2B type 1-J 9606
121 3REI 4 D, H Histone H2B 1.1 8355
122 1P3B 5 D, H Histone H2B 8355
123 3WKJ 4 D, H Histone H2B type 1-A 9606
124 3AZK 4 D, H Histone H2B type 1-J 9606
125 4J8X 4 D, H Histone H2B 1.1 8355
126 3LEL 4 D, H, N, R Histone H2B 1.1 8355
127 3KUY 4 D, H Histone H2B 8355
128 4R8P 4 D, H Histone H2B 1.1 8355
129 3AZM 4 D, H Histone H2B type 1-J 9606
130 3X1U 5 D, H Histone H2B type 1-B 9606
131 3MGS 4 D, H Histone H2B 1.1 8355
132 3WA9 4 D, H Histone H2B type 1-J 9606
133 3C1C 4 D, H Histone 2, H2bf 8364
134 3AZH 4 D, H Histone H2B type 1-J 9606
135 5B40 4 D, H Histone H2B type 1-J 9606
136 3WAA 4 D, H Histone H2B type 1-J 9606
137 5CPI 4 D, H Histone H2B type 1-J 9606
138 3W99 4 D, H Histone H2B type 1-J 9606
139 3AZE 4 D, H Histone H2B type 1-J 9606
140 6LA8 4 D, H, N, R Histone H2B type 1-J 9606
141 3W96 4 D, H Histone H2B type 1-J 9606
142 6OM3 4 D, H, P, T Histone H2B 1.1 8355
143 5XM1 4 D, H Histone H2B type 3-A 10090
144 6K1J 4 D, H Histone H2B type 1-J 9606
145 5CPJ 4 D, H Histone H2B type 1-J 9606
146 6LA9 4 D, H, N, R Histone H2B type 1-J 9606
147 5B24 4 D, H Histone H2B type 1-J 9606
148 2HIO 2 B PROTEIN (HISTONE H2B) 9031
149 4QLC 6 D, H Histone H2B 7227
150 4LD9 4 D, H Histone H2B 1.1 8355
151 3O62 4 D, H Histone H2B 1.1 8355
152 6M44 4 D, H, N, R Histone H2B type 1-J 9606
153 6KXV 4 D, H Histone H2B type 1-J 9606
154 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
155 4YM5 4 D, H Histone H2B type 1-J 9606
156 4YM6 4 D, H Histone H2B type 1-J 9606
157 2FJ7 6 D, H Histone H2B 8355
158 3W98 4 D, H Histone H2B type 1-J 9606
159 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
160 6M3V 4 D, H, N, R Histone H2B type 1-J 9606
161 3AN2 4 D, H Histone H2B type 1-J 9606
162 6VYP 4 D, H, d, h Histone H2B 1.1 8355
163 3B6F 6 D, H Histone H2B 1.1 8355
164 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
165 3B6G 6 D, H Histone H2B 1.1 8355
166 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
167 3KXB 4 D, H Histone H2B 1.1 8355
168 5HQ2 4 H Histone H2B 1.1 8355
169 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
170 5OXV 2 D, H, N, R Histone H2B 1.1 8355
171 1ZBB 6 D, H, d, h Histone H2B.1 8355
172 7K63 4 D, H Histone H2B type 1-J 9606
173 7K5X 4 D, H Histone H2B type 1-J 9606
174 7K5Y 4 D, H Histone H2B type 1-J 9606
175 7K60 4 D, H Histone H2B type 1-J 9606
176 7K61 4 D, H Histone H2B type 1-J 9606
177 7CRO 4 D, H Histone H2B 8364
178 7CRP 4 D, H Histone H2B 8364
179 7CRQ 4 D, H Histone H2B 8364
180 7CRR 4 D, H Histone H2B 8364
181 7A08 5 c, g Histone H2B type 1-C/E/F/G/I 9606
182 7JO9 4 D, H Histone H2B type 1-C/E/F/G/I 9606
183 7JOA 4 D, H Histone H2B type 1-C/E/F/G/I 9606
184 6XJD 4 D, H Histone H2B type 1-C/E/F/G/I 9606
185 6X59 4 D, H Histone H2B type 1-C/E/F/G/I 9606
186 6X5A 4 D, H Histone H2B type 1-C/E/F/G/I 9606
187 6X0N 4 D, H, d, h Histone H2B 1.1 8355
188 6WZ5 4 D, H Histone H2B 1.1 8355
189 6WZ9 4 D, H Histone H2B 1.1 8355
190 7C0M 4 D, H, d, h Histone H2B type 1-J 9606
191 6YOV 4 D, H Histone H2B type 1-J 9606
192 6M4H 6 D, H Histone H2B type 2-E 9606
193 6M4D 4 D, H Histone H2B type 2-E 9606
194 6M4G 5 D, H Histone H2B type 2-E 9606
195 6VZ4 4 D, H Histone H2B 8355
196 6Y5D 4 D, H, P, T Histone H2B type 1-K 9606
197 6LTJ 4 D, H Histone H2B 8355
198 6VEN 4 D, H Histone H2B 1.1 8355
199 6V92 26 d, h Histone H2B type 1-K 9606
200 6TEM 4 D, H Histone H2B 1.1 8355
201 6TDA 4 D, H Histone H2B 1.1 8355
202 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
203 6T9L 4 D Histone H2B 1.1 8355
204 6T9L 5 H Histone H2B 8355
205 6USJ 6 D, H, N, R Histone H2B type 1-J 9606
206 6T90 4 D, H Histone H2B type 1-J 9606
207 6T93 4 D, H Histone H2B type 1-J 9606
208 6T79 4 D, H Histone H2B type 1-K 9606
209 6T7A 4 D, H Histone H2B type 1-K 9606
210 6T7B 4 D, H Histone H2B type 1-K 9606
211 6T7C 4 D, H Histone H2B type 1-K 9606
212 6T7D 4 D, H Histone H2B type 1-K 9606
213 6UPK 4 D Histone H2B 9606
214 6UPL 4 D, L Histone H2B 9606
215 6L49 4 D, H, N, R, V, Z Histone H2B type 1-J 9606
216 6L4A 4 D, H, N, R, V, Z Histone H2B type 1-J 9606
217 6UGM 4 D Histone H2B 8355
218 6UGM 5 H Histone H2B 1.1 8355
219 6UH5 4 D Histone H2B 8355
220 6UH5 5 H Histone H2B 8355
221 6KW4 20 P, T Histone H4 8355
222 6KW5 18 U, Y Histone H4 8355
223 6KW3 20 P, T Histone H4 8355
224 6SEG 4 D, H Histone H2B type 1-C/E/F/G/I 9606
225 6SE0 4 D, H Histone H2B type 1-C/E/F/G/I 9606
226 6SE6 4 D, H Histone H2B type 1-C/E/F/G/I 9606
227 6SEE 4 D, H Histone H2B type 1-C/E/F/G/I 9606
228 6SEF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
229 6PX1 4 D, H Histone H2B 1.1 8355
230 6PX3 4 D, H Histone H2B 1.1 8355
231 6PWV 7 J, N Histone H2B 1.1 8355
232 6PWW 7 J, N Histone H2B 1.1 8355
233 6PWX 5 J, N Histone H2B 1.1 8355
234 6PWE 4 D, H Histone H2B 7227
235 6PWF 4 D, H Histone H2B 7227
236 6KIU 4 D, H Histone H2B 1.1 8355
237 6KIV 4 D, H Histone H2B 1.1 8355
238 6KIW 4 D, H Histone H2B 1.1 8355
239 6KIX 4 D, H Histone H2B 1.1 8355
240 6KIZ 4 D, H Histone H2B 1.1 8355
241 6S01 4 D, H Histone H2B 1.1 8355
242 6RYU 4 D, H Histone H2B 1.1 8355
243 6PA7 4 D, H Histone H2B 1.1 8355
244 6RYR 4 D, H Histone H2B 1.1 8355
245 6K1P 4 D, H Histone H2B 1.1 8355
246 6RNY 4 D, H Histone H2B type 1-C/E/F/G/I 9606
247 6JYL 4 D, H Histone H2B 1.1 8355
248 6R8Y 4 D, H Histone H2B type 1-J 9606
249 6R8Z 4 D, H Histone H2B type 1-J 9606
250 6R90 4 D, H Histone H2B type 1-J 9606
251 6R91 4 D, H Histone H2B type 1-J 9606
252 6R92 7 D, H Histone H2B type 1-J 9606
253 6R93 6 D, H Histone H2B type 1-J 9606
254 6R94 6 D, H Histone H2B type 1-J 9606
255 6R1U 4 D, H Histone H2B 1.1 8355
256 6R25 7 D, H H2B 8355
257 6O96 4 D, H Histone H2B 1.1 8355
258 6R0C 4 D, H Histone H2B type 1-C/E/F/G/I 9606
259 6O1D 4 D, H Histone H2B type 1-J 9606
260 6NZO 4 D, H Histone H2B 1.1 8355
261 6J99 4 D, H Histone H2B 1.1 8355
262 6NQA 5 D, H Histone H2B 1.1 8355
263 6NOG 4 D, H Histone H2B 1.1 8355
264 6NN6 4 D, H Histone H2B 1.1 8355
265 6J4W 22 d, h Histone H2B type 1-J 9606
266 6J4X 22 d, h Histone H2B type 1-J 9606
267 6J4Y 22 d, h Histone H2B type 1-J 9606
268 6J4Z 21 d, h Histone H2B type 1-J 9606
269 6J50 21 d, h Histone H2B type 1-J 9606
270 6J51 22 d, h Histone H2B type 1-J 9606
271 6NJ9 3 D, H Histone H2B 1.1 8355
272 6I84 6 R, W Histone H2B 1.1 8355
273 6IRO 5 D, H Histone H2B 1.1 8355
274 6IR9 22 d, h Histone H2B type 1-J 9606
275 6INQ 19 d, h Histone H2B type 1-J 9606
276 6HTS 8 L, P Histone H2B type 1-J 9606
277 6E0C 4 D, H Histone H2B type 1-J 9606
278 6E0P 4 D, H Histone H2B type 1-J 9606
279 6DZT 4 D, H Histone H2B 7227
280 6A5O 19 d, h Histone H2B type 1-J 9606
281 6A5P 19 d, h Histone H2B type 1-J 9606
282 6A5R 19 d, h Histone H2B type 1-J 9606
283 6A5T 19 d, h Histone H2B type 1-J 9606
284 6A5U 19 d, h Histone H2B, Histone H2B type 1-J 9606
285 6A5L 19 d, h Histone H2B type 1-J 9606
286 6G0L 4 D, H Histone H4 8355
287 6FTX 4 D, H Histone H2B 8364
288 6FML 12 P, T Histone H2B type 1-C/E/F/G/I 9606
289 5Z3L 4 D, H Histone H2B 1.1 8355
290 5Z3O 4 D, H Histone H2B 1.1 8355
291 5Z3U 5 D, H Histone H2B 1.1 8355
292 5Z3V 5 D, H Histone H2B 1.1 8355
293 6C0W 4 D, H Histone H2B 9606
294 6BUZ 4 D, H Histone H2B 9606
295 6ESF 4 D, H Histone H2B 1.1 8355
296 6ESG 4 D, H Histone H2B 1.1 8355
297 6ESH 4 D, H Histone H2B 1.1 8355
298 6ESI 4 D Histone H2B 1.1 8355
299 6ESI 5 H Histone H2B 1.1 8355
300 5O9G 4 D Histone H2B 1.1 8355
301 5O9G 5 H Histone H2B 1.1 8355
302 5X0X 4 D, H Histone H2B 1.1 8355
303 5X0Y 4 D, H Histone H2B 1.1 8355
304 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
305 2RVQ 2 D Histone H2B type 1-J 9606
306 3C9K 2 B, F Histone H2B 7 9031