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 5BT1 3 D Histone H2B.1 4932
52 5XF6 4 D, H Histone H2B 1.1 8355
53 3MGP 4 D, H Histone H2B 1.1 8355
54 3MVD 4 D, H Histone H2B 1.1 8355
55 4J8U 4 D, H Histone H2B 1.1 8355
56 4WU9 4 D, H Histone H2B 1.1 8355
57 3REH 4 D, H Histone H2B 1.1 8355
58 3AZL 4 D, H Histone H2B type 1-J 9606
59 5Z23 4 D, H Histone H2B type 1-J Se-Met-substituted H2B 9606
60 6N1Z 3 C, F Histone H2B 1.1 HISTONE H2B 1.1 8355
61 3AFA 4 D, H Histone H2B type 1-J 9606
62 5E5A 5 D, H Histone H2B 1.1 8355
63 3REJ 4 D, H Histone H2B 1.1 8355
64 3AZF 4 D, H Histone H2B type 1-J 9606
65 5GTC 4 D, H Histone H2B type 1-J 9606
66 1P3P 5 D, H Histone H2B 8355
67 3AV1 4 D, H Histone H2B type 1-J 9606
68 1M1A 5 D, H Histone H2B.1 8355
69 5CPK 4 D, H Histone H2B type 1-J 9606
70 5AY8 4 D, H Histone H2B type 1-J 9606
71 3MNN 4 D, H Histone H2B 1.1 8355
72 1P3G 5 D, H Histone H2B 8355
73 4J8W 4 D, H Histone H2B 1.1 8355
74 1P34 5 D, H Histone H2B 8355
75 5XF3 4 D, H Histone H2B type 1-J 9606
76 3X1V 5 D, H Histone H2B type 1-A 10090
77 5ONG 6 D, H Histone H2B 1.1 8355
78 5ONW 6 D, H Histone H2B 1.1 8355
79 5DNM 4 D, H Histone H2B 1.1 8355
80 6K1I 4 D, H Histone H2B type 1-J 9606
81 3MGQ 4 D, H Histone H2B 1.1 8355
82 3WTP 4 D, H Histone H2B type 1-J 9606
83 3X1T 5 D, H Histone H2B type 1-A 10090
84 2NZD 6 D, H Histone H2B 8355
85 3A6N 4 D, H Histone H2B type 1-J 9606
86 5DNN 4 D, H Histone H2B 1.1 8355
87 5GT3 4 D, H Histone H2B type 1-A 9606
88 5GT0 4 D, H Histone H2B type 1-J 9606
89 3LJA 4 D, H Histone H2B 1.1 8355
90 3AZI 4 D, H Histone H2B type 1-J 9606
91 3TU4 4 D, H Histone H2B 1.1 8355
92 1P3O 5 D, H Histone H2B 8355
93 1KX4 5 D, H histone H2B.2 8355
94 3AZN 4 D, H Histone H2B type 1-J 9606
95 1P3M 5 D, H Histone H2B 8355
96 4J8V 4 D, H Histone H2B 1.1 8355
97 5B33 4 D, H Histone H2B type 1-J 9606
98 3X1S 4 D, H Histone H2B type 1-B 9606
99 3LZ0 4 D, H Histone H2B 1.1 8355
100 1P3F 5 D, H Histone H2B 8355
101 1P3K 5 D, H Histone H2B 8355
102 5B2I 4 D, H Histone H2B type 1-J 9606
103 1P3A 5 D, H Histone H2B 8355
104 3LZ1 4 D, H Histone H2B 1.1 8355
105 5GXQ 4 D, H Histone H2B type 1-J 9606
106 2F8N 4 D Histone 3, H2ba 10090
107 2F8N 5 H Histone H2B.1 8355
108 4Z5T 4 D, H Histone H2B type 1-J 9606
109 1U35 5 D, H histone 3, H2ba 10090
110 5XM0 4 D, H Histone H2B type 3-A 10090
111 3AV2 4 D, H Histone H2B type 1-J 9606
112 3AYW 4 D, H Histone H2B type 1-J 9606
113 5XF5 4 D, H Histone H2B type 1-J 9606
114 3AZJ 4 D, H Histone H2B type 1-J 9606
115 3REK 4 D, H Histone H2B 1.1 8355
116 4KGC 4 D, H Histone H2B 1.1 8355
117 1ZLA 5 D, H histone H2B 8355
118 5GSU 4 D, H Histone H2B type 1-A 9606
119 5XF4 4 D, H Histone H2B type 1-J 9606
120 3REL 4 D, H Histone H2B 1.1 8355
121 5GSE 4 D, H, N Histone H2B type 1-J 9606
122 3REI 4 D, H Histone H2B 1.1 8355
123 1P3B 5 D, H Histone H2B 8355
124 3WKJ 4 D, H Histone H2B type 1-A 9606
125 4KUD 4 D, H Histone H2B.1 4932
126 3AZK 4 D, H Histone H2B type 1-J 9606
127 4J8X 4 D, H Histone H2B 1.1 8355
128 3LEL 4 D, H, N, R Histone H2B 1.1 8355
129 3KUY 4 D, H Histone H2B 8355
130 4R8P 4 D, H Histone H2B 1.1 8355
131 3AZM 4 D, H Histone H2B type 1-J 9606
132 3X1U 5 D, H Histone H2B type 1-B 9606
133 3MGS 4 D, H Histone H2B 1.1 8355
134 3WA9 4 D, H Histone H2B type 1-J 9606
135 1ID3 5 D, H HISTONE H2B.2 4932
136 3C1C 4 D, H Histone 2, H2bf 8364
137 3AZH 4 D, H Histone H2B type 1-J 9606
138 5B40 4 D, H Histone H2B type 1-J 9606
139 3WAA 4 D, H Histone H2B type 1-J 9606
140 5CPI 4 D, H Histone H2B type 1-J 9606
141 4JJN 4 D, H Histone H2B.2 4932
142 3W99 4 D, H Histone H2B type 1-J 9606
143 3AZE 4 D, H Histone H2B type 1-J 9606
144 6LA8 4 D, H, N, R Histone H2B type 1-J 9606
145 3W96 4 D, H Histone H2B type 1-J 9606
146 6OM3 4 D, H, P, T Histone H2B 1.1 8355
147 5XM1 4 D, H Histone H2B type 3-A 10090
148 6K1J 4 D, H Histone H2B type 1-J 9606
149 5CPJ 4 D, H Histone H2B type 1-J 9606
150 6LA9 4 D, H, N, R Histone H2B type 1-J 9606
151 5B24 4 D, H Histone H2B type 1-J 9606
152 2HIO 2 B PROTEIN (HISTONE H2B) 9031
153 4QLC 6 D, H Histone H2B 7227
154 4LD9 4 D, H Histone H2B 1.1 8355
155 3O62 4 D, H Histone H2B 1.1 8355
156 6M44 4 D, H, N, R Histone H2B type 1-J 9606
157 6KXV 4 D, H Histone H2B type 1-J 9606
158 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
159 4YM5 4 D, H Histone H2B type 1-J 9606
160 4YM6 4 D, H Histone H2B type 1-J 9606
161 2FJ7 6 D, H Histone H2B 8355
162 3W98 4 D, H Histone H2B type 1-J 9606
163 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
164 6M3V 4 D, H, N, R Histone H2B type 1-J 9606
165 3AN2 4 D, H Histone H2B type 1-J 9606
166 6VYP 4 D, H, d, h Histone H2B 1.1 8355
167 3B6F 6 D, H Histone H2B 1.1 8355
168 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
169 3B6G 6 D, H Histone H2B 1.1 8355
170 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
171 3KXB 4 D, H Histone H2B 1.1 8355
172 5HQ2 4 H Histone H2B 1.1 8355
173 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
174 5OXV 2 D, H, N, R Histone H2B 1.1 8355
175 1ZBB 6 D, H, d, h Histone H2B.1 8355
176 7K63 4 D, H Histone H2B type 1-J 9606
177 7K5X 4 D, H Histone H2B type 1-J 9606
178 7K5Y 4 D, H Histone H2B type 1-J 9606
179 7K60 4 D, H Histone H2B type 1-J 9606
180 7K61 4 D, H Histone H2B type 1-J 9606
181 7CRO 4 D, H Histone H2B 8364
182 7CRP 4 D, H Histone H2B 8364
183 7CRQ 4 D, H Histone H2B 8364
184 7CRR 4 D, H Histone H2B 8364
185 7A08 5 c, g Histone H2B type 1-C/E/F/G/I 9606
186 7JO9 4 D, H Histone H2B type 1-C/E/F/G/I 9606
187 7JOA 4 D, H Histone H2B type 1-C/E/F/G/I 9606
188 6XJD 4 D, H Histone H2B type 1-C/E/F/G/I 9606
189 6X59 4 D, H Histone H2B type 1-C/E/F/G/I 9606
190 6X5A 4 D, H Histone H2B type 1-C/E/F/G/I 9606
191 6X0N 4 D, H, d, h Histone H2B 1.1 8355
192 6WZ5 4 D, H Histone H2B 1.1 8355
193 6WZ9 4 D, H Histone H2B 1.1 8355
194 7C0M 4 D, H, d, h Histone H2B type 1-J 9606
195 6YOV 4 D, H Histone H2B type 1-J 9606
196 6M4H 6 D, H Histone H2B type 2-E 9606
197 6M4D 4 D, H Histone H2B type 2-E 9606
198 6M4G 5 D, H Histone H2B type 2-E 9606
199 6VZ4 4 D, H Histone H2B 8355
200 6Y5D 4 D, H, P, T Histone H2B type 1-K 9606
201 6LTJ 4 D, H Histone H2B 8355
202 6VEN 4 D, H Histone H2B 1.1 8355
203 6V92 26 d, h Histone H2B type 1-K 9606
204 6TEM 4 D, H Histone H2B 1.1 8355
205 6TDA 4 D, H Histone H2B 1.1 8355
206 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
207 6T9L 4 D Histone H2B 1.1 8355
208 6T9L 5 H Histone H2B 8355
209 6USJ 6 D, H, N, R Histone H2B type 1-J 9606
210 6T90 4 D, H Histone H2B type 1-J 9606
211 6T93 4 D, H Histone H2B type 1-J 9606
212 6T79 4 D, H Histone H2B type 1-K 9606
213 6T7A 4 D, H Histone H2B type 1-K 9606
214 6T7B 4 D, H Histone H2B type 1-K 9606
215 6T7C 4 D, H Histone H2B type 1-K 9606
216 6T7D 4 D, H Histone H2B type 1-K 9606
217 6UPH 4 D, H Histone H2B.1 28985
218 6UPK 4 D Histone H2B 9606
219 6UPL 4 D, L Histone H2B 9606
220 6L49 4 D, H, N, R, V, Z Histone H2B type 1-J 9606
221 6L4A 4 D, H, N, R, V, Z Histone H2B type 1-J 9606
222 6UGM 4 D Histone H2B 8355
223 6UGM 5 H Histone H2B 1.1 8355
224 6UH5 4 D Histone H2B 8355
225 6UH5 5 H Histone H2B 8355
226 6KW4 20 P, T Histone H4 8355
227 6KW5 18 U, Y Histone H4 8355
228 6KW3 20 P, T Histone H4 8355
229 6SEG 4 D, H Histone H2B type 1-C/E/F/G/I 9606
230 6SE0 4 D, H Histone H2B type 1-C/E/F/G/I 9606
231 6SE6 4 D, H Histone H2B type 1-C/E/F/G/I 9606
232 6SEE 4 D, H Histone H2B type 1-C/E/F/G/I 9606
233 6SEF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
234 6PX1 4 D, H Histone H2B 1.1 8355
235 6PX3 4 D, H Histone H2B 1.1 8355
236 6PWV 7 J, N Histone H2B 1.1 8355
237 6PWW 7 J, N Histone H2B 1.1 8355
238 6PWX 5 J, N Histone H2B 1.1 8355
239 6PWE 4 D, H Histone H2B 7227
240 6PWF 4 D, H Histone H2B 7227
241 6KIU 4 D, H Histone H2B 1.1 8355
242 6KIV 4 D, H Histone H2B 1.1 8355
243 6KIW 4 D, H Histone H2B 1.1 8355
244 6KIX 4 D, H Histone H2B 1.1 8355
245 6KIZ 4 D, H Histone H2B 1.1 8355
246 6S01 4 D, H Histone H2B 1.1 8355
247 6RYU 4 D, H Histone H2B 1.1 8355
248 6PA7 4 D, H Histone H2B 1.1 8355
249 6RYR 4 D, H Histone H2B 1.1 8355
250 6K1P 4 D, H Histone H2B 1.1 8355
251 6RNY 4 D, H Histone H2B type 1-C/E/F/G/I 9606
252 6JYL 4 D, H Histone H2B 1.1 8355
253 6R8Y 4 D, H Histone H2B type 1-J 9606
254 6R8Z 4 D, H Histone H2B type 1-J 9606
255 6R90 4 D, H Histone H2B type 1-J 9606
256 6R91 4 D, H Histone H2B type 1-J 9606
257 6R92 7 D, H Histone H2B type 1-J 9606
258 6R93 6 D, H Histone H2B type 1-J 9606
259 6R94 6 D, H Histone H2B type 1-J 9606
260 6R1U 4 D, H Histone H2B 1.1 8355
261 6R25 7 D, H H2B 8355
262 6O96 4 D, H Histone H2B 1.1 8355
263 6R0C 4 D, H Histone H2B type 1-C/E/F/G/I 9606
264 6O1D 4 D, H Histone H2B type 1-J 9606
265 6NZO 4 D, H Histone H2B 1.1 8355
266 6J99 4 D, H Histone H2B 1.1 8355
267 6NQA 5 D, H Histone H2B 1.1 8355
268 6NOG 4 D, H Histone H2B 1.1 8355
269 6NN6 4 D, H Histone H2B 1.1 8355
270 6J4W 22 d, h Histone H2B type 1-J 9606
271 6J4X 22 d, h Histone H2B type 1-J 9606
272 6J4Y 22 d, h Histone H2B type 1-J 9606
273 6J4Z 21 d, h Histone H2B type 1-J 9606
274 6J50 21 d, h Histone H2B type 1-J 9606
275 6J51 22 d, h Histone H2B type 1-J 9606
276 6NJ9 3 D, H Histone H2B 1.1 8355
277 6I84 6 R, W Histone H2B 1.1 8355
278 6IRO 5 D, H Histone H2B 1.1 8355
279 6IR9 22 d, h Histone H2B type 1-J 9606
280 6INQ 19 d, h Histone H2B type 1-J 9606
281 6HTS 8 L, P Histone H2B type 1-J 9606
282 6E0C 4 D, H Histone H2B type 1-J 9606
283 6E0P 4 D, H Histone H2B type 1-J 9606
284 6DZT 4 D, H Histone H2B 7227
285 6A5O 19 d, h Histone H2B type 1-J 9606
286 6A5P 19 d, h Histone H2B type 1-J 9606
287 6A5R 19 d, h Histone H2B type 1-J 9606
288 6A5T 19 d, h Histone H2B type 1-J 9606
289 6A5U 19 d, h Histone H2B, Histone H2B type 1-J 9606
290 6A5L 19 d, h Histone H2B type 1-J 9606
291 6GEN 5 G, H Histone H2B.1 4932
292 6GEJ 5 G, H Histone H2B.1 4932
293 6G0L 4 D, H Histone H4 8355
294 6FTX 4 D, H Histone H2B 8364
295 6FML 12 P, T Histone H2B type 1-C/E/F/G/I 9606
296 5Z3L 4 D, H Histone H2B 1.1 8355
297 5Z3O 4 D, H Histone H2B 1.1 8355
298 5Z3U 5 D, H Histone H2B 1.1 8355
299 5Z3V 5 D, H Histone H2B 1.1 8355
300 6C0W 4 D, H Histone H2B 9606
301 6BUZ 4 D, H Histone H2B 9606
302 6ESF 4 D, H Histone H2B 1.1 8355
303 6ESG 4 D, H Histone H2B 1.1 8355
304 6ESH 4 D, H Histone H2B 1.1 8355
305 6ESI 4 D Histone H2B 1.1 8355
306 6ESI 5 H Histone H2B 1.1 8355
307 5O9G 4 D Histone H2B 1.1 8355
308 5O9G 5 H Histone H2B 1.1 8355
309 5X0X 4 D, H Histone H2B 1.1 8355
310 5X0Y 4 D, H Histone H2B 1.1 8355
311 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
312 2RVQ 2 D Histone H2B type 1-J 9606
313 3C9K 2 B, F Histone H2B 7 9031