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 9 3614
95 % 8 14 3260
90 % 9 14 2889
70 % 8 11 4450
50 % 234 335 67
40 % 234 335 87
30 % 234 312 94
Entity #2 | Chains: B,F
Histone H4 protein, length: 103 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 214 293 9
95 % 236 318 17
90 % 243 327 19
70 % 244 326 25
50 % 244 326 58
40 % 244 326 79
30 % 244 326 85
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 6039
95 % 209 293 19
90 % 192 266 45
70 % 205 284 40
50 % 218 297 73
40 % 218 297 95
30 % 218 297 98
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 9 1587
95 % 163 199 76
90 % 211 288 27
70 % 219 299 32
50 % 224 312 68
40 % 224 306 90
30 % 224 331 96
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 36402
95 % 1 3 32849
90 % 1 3 31500
70 % 1 3 28196
50 % 1 3 24679
40 % 1 3 22546
30 % 1 3 18681

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 5OMX 6 D, H Histone H2B 1.1 8355
28 6JR1 4 D, H Histone H2B type 1-J 9606
29 5F99 4 D, H Histone H2B 1.1 8355
30 5Z30 4 D, H Histone H2B type 1-J 9606
31 5JRG 4 D, H Histone H2B type 1-J 9606
32 3UT9 4 D, H Histone H2B 1.1 8355
33 5B32 4 D, H Histone H2B type 1-J 9606
34 4WU8 6 D, H Histone H2B 1.1 8355
35 1P3I 5 D, H Histone H2B 8355
36 3MGR 4 D, H Histone H2B 1.1 8355
37 1F66 5 D, H HISTONE H2B 8355
38 3AZG 4 D, H Histone H2B type 1-J 9606
39 1M18 5 D, H Histone H2B.1 8355
40 5B2J 4 D, H Histone H2B type 1-J 9606
41 1P3L 5 D, H Histone H2B 8355
42 1EQZ 3 B, F PROTEIN (HISTONE H2B) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
43 5B0Y 4 D, H Histone H2B type 1-J 9606
44 6JR0 4 D, H Histone H2B type 1-J 9606
45 2CV5 5 D, H Histone H2B K 9606
46 5CP6 6 D, H Histone H2B 1.1 8355
47 5ZBX 4 D, H Histone H2B type 1-J 9606
48 5XF6 4 D, H Histone H2B 1.1 8355
49 3MGP 4 D, H Histone H2B 1.1 8355
50 3MVD 4 D, H Histone H2B 1.1 8355
51 4J8U 4 D, H Histone H2B 1.1 8355
52 4WU9 4 D, H Histone H2B 1.1 8355
53 3REH 4 D, H Histone H2B 1.1 8355
54 3AZL 4 D, H Histone H2B type 1-J 9606
55 5Z23 4 D, H Histone H2B type 1-J Se-Met-substituted H2B 9606
56 6N1Z 3 C, F Histone H2B 1.1 HISTONE H2B 1.1 8355
57 3AFA 4 D, H Histone H2B type 1-J 9606
58 5E5A 5 D, H Histone H2B 1.1 8355
59 3REJ 4 D, H Histone H2B 1.1 8355
60 3AZF 4 D, H Histone H2B type 1-J 9606
61 5GTC 4 D, H Histone H2B type 1-J 9606
62 1P3P 5 D, H Histone H2B 8355
63 3AV1 4 D, H Histone H2B type 1-J 9606
64 1M1A 5 D, H Histone H2B.1 8355
65 5CPK 4 D, H Histone H2B type 1-J 9606
66 5AY8 4 D, H Histone H2B type 1-J 9606
67 3MNN 4 D, H Histone H2B 1.1 8355
68 1P3G 5 D, H Histone H2B 8355
69 4J8W 4 D, H Histone H2B 1.1 8355
70 1P34 5 D, H Histone H2B 8355
71 5XF3 4 D, H Histone H2B type 1-J 9606
72 5ONG 6 D, H Histone H2B 1.1 8355
73 5ONW 6 D, H Histone H2B 1.1 8355
74 5DNM 4 D, H Histone H2B 1.1 8355
75 6K1I 4 D, H Histone H2B type 1-J 9606
76 3MGQ 4 D, H Histone H2B 1.1 8355
77 3WTP 4 D, H Histone H2B type 1-J 9606
78 2NZD 6 D, H Histone H2B 8355
79 3A6N 4 D, H Histone H2B type 1-J 9606
80 5DNN 4 D, H Histone H2B 1.1 8355
81 5GT0 4 D, H Histone H2B type 1-J 9606
82 3LJA 4 D, H Histone H2B 1.1 8355
83 3AZI 4 D, H Histone H2B type 1-J 9606
84 3TU4 4 D, H Histone H2B 1.1 8355
85 1P3O 5 D, H Histone H2B 8355
86 1KX4 5 D, H histone H2B.2 8355
87 3AZN 4 D, H Histone H2B type 1-J 9606
88 1P3M 5 D, H Histone H2B 8355
89 4J8V 4 D, H Histone H2B 1.1 8355
90 5B33 4 D, H Histone H2B type 1-J 9606
91 3X1S 4 D, H Histone H2B type 1-B 9606
92 3LZ0 4 D, H Histone H2B 1.1 8355
93 1P3F 5 D, H Histone H2B 8355
94 1P3K 5 D, H Histone H2B 8355
95 5B2I 4 D, H Histone H2B type 1-J 9606
96 1P3A 5 D, H Histone H2B 8355
97 3LZ1 4 D, H Histone H2B 1.1 8355
98 5GXQ 4 D, H Histone H2B type 1-J 9606
99 2F8N 4 D Histone 3, H2ba 10090
100 2F8N 5 H Histone H2B.1 8355
101 4Z5T 4 D, H Histone H2B type 1-J 9606
102 1U35 5 D, H histone 3, H2ba 10090
103 5XM0 4 D, H Histone H2B type 3-A 10090
104 3AV2 4 D, H Histone H2B type 1-J 9606
105 3AYW 4 D, H Histone H2B type 1-J 9606
106 5XF5 4 D, H Histone H2B type 1-J 9606
107 3AZJ 4 D, H Histone H2B type 1-J 9606
108 3REK 4 D, H Histone H2B 1.1 8355
109 4KGC 4 D, H Histone H2B 1.1 8355
110 1ZLA 5 D, H histone H2B 8355
111 5XF4 4 D, H Histone H2B type 1-J 9606
112 3REL 4 D, H Histone H2B 1.1 8355
113 5GSE 4 D, H, N Histone H2B type 1-J 9606
114 3REI 4 D, H Histone H2B 1.1 8355
115 1P3B 5 D, H Histone H2B 8355
116 3AZK 4 D, H Histone H2B type 1-J 9606
117 4J8X 4 D, H Histone H2B 1.1 8355
118 3LEL 4 D, H, N, R Histone H2B 1.1 8355
119 3KUY 4 D, H Histone H2B 8355
120 4R8P 4 D, H Histone H2B 1.1 8355
121 3AZM 4 D, H Histone H2B type 1-J 9606
122 3X1U 5 D, H Histone H2B type 1-B 9606
123 3MGS 4 D, H Histone H2B 1.1 8355
124 3WA9 4 D, H Histone H2B type 1-J 9606
125 3C1C 4 D, H Histone 2, H2bf 8364
126 3AZH 4 D, H Histone H2B type 1-J 9606
127 5B40 4 D, H Histone H2B type 1-J 9606
128 3WAA 4 D, H Histone H2B type 1-J 9606
129 5CPI 4 D, H Histone H2B type 1-J 9606
130 3W99 4 D, H Histone H2B type 1-J 9606
131 3AZE 4 D, H Histone H2B type 1-J 9606
132 6LA8 4 D, H, N, R Histone H2B type 1-J 9606
133 3W96 4 D, H Histone H2B type 1-J 9606
134 6OM3 4 D, H, P, T Histone H2B 1.1 8355
135 5XM1 4 D, H Histone H2B type 3-A 10090
136 6K1J 4 D, H Histone H2B type 1-J 9606
137 5CPJ 4 D, H Histone H2B type 1-J 9606
138 6LA9 4 D, H, N, R Histone H2B type 1-J 9606
139 5B24 4 D, H Histone H2B type 1-J 9606
140 2HIO 2 B PROTEIN (HISTONE H2B) 9031
141 4LD9 4 D, H Histone H2B 1.1 8355
142 3O62 4 D, H Histone H2B 1.1 8355
143 6M44 4 D, H, N, R Histone H2B type 1-J 9606
144 6KXV 4 D, H Histone H2B type 1-J 9606
145 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
146 4YM5 4 D, H Histone H2B type 1-J 9606
147 4YM6 4 D, H Histone H2B type 1-J 9606
148 2FJ7 6 D, H Histone H2B 8355
149 3W98 4 D, H Histone H2B type 1-J 9606
150 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
151 6M3V 4 D, H, N, R Histone H2B type 1-J 9606
152 3AN2 4 D, H Histone H2B type 1-J 9606
153 6VYP 4 D, H, d, h Histone H2B 1.1 8355
154 3B6F 6 D, H Histone H2B 1.1 8355
155 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
156 3B6G 6 D, H Histone H2B 1.1 8355
157 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
158 3KXB 4 D, H Histone H2B 1.1 8355
159 5HQ2 4 H Histone H2B 1.1 8355
160 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
161 5OXV 2 D, H, N, R Histone H2B 1.1 8355
162 1ZBB 6 D, H, d, h Histone H2B.1 8355
163 7CRO 4 D, H Histone H2B 8364
164 7CRP 4 D, H Histone H2B 8364
165 7CRQ 4 D, H Histone H2B 8364
166 7CRR 4 D, H Histone H2B 8364
167 7A08 5 c, g Histone H2B type 1-C/E/F/G/I 9606
168 7JO9 4 D, H Histone H2B type 1-C/E/F/G/I 9606
169 7JOA 4 D, H Histone H2B type 1-C/E/F/G/I 9606
170 6XJD 4 D, H Histone H2B type 1-C/E/F/G/I 9606
171 6X59 4 D, H Histone H2B type 1-C/E/F/G/I 9606
172 6X5A 4 D, H Histone H2B type 1-C/E/F/G/I 9606
173 6X0N 4 D, H, d, h Histone H2B 1.1 8355
174 6WZ5 4 D, H Histone H2B 1.1 8355
175 6WZ9 4 D, H Histone H2B 1.1 8355
176 7C0M 4 D, H, d, h Histone H2B type 1-J 9606
177 6YOV 4 D, H Histone H2B type 1-J 9606
178 6M4H 6 D, H Histone H2B type 2-E 9606
179 6M4D 4 D, H Histone H2B type 2-E 9606
180 6M4G 5 D, H Histone H2B type 2-E 9606
181 6Y5D 4 D, H, P, T Histone H2B type 1-K 9606
182 6LTJ 4 D, H Histone H2B 8355
183 6VEN 4 D, H Histone H2B 1.1 8355
184 6V92 26 d, h Histone H2B type 1-K 9606
185 6TEM 4 D, H Histone H2B 1.1 8355
186 6TDA 4 D, H Histone H2B 1.1 8355
187 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
188 6T9L 4 D Histone H2B 1.1 8355
189 6T9L 5 H Histone H2B 8355
190 6USJ 6 D, H, N, R Histone H2B type 1-J 9606
191 6T90 4 D, H Histone H2B type 1-J 9606
192 6T93 4 D, H Histone H2B type 1-J 9606
193 6T79 4 D, H Histone H2B type 1-K 9606
194 6T7A 4 D, H Histone H2B type 1-K 9606
195 6T7B 4 D, H Histone H2B type 1-K 9606
196 6T7C 4 D, H Histone H2B type 1-K 9606
197 6T7D 4 D, H Histone H2B type 1-K 9606
198 6UPK 4 D Histone H2B 9606
199 6UPL 4 D, L Histone H2B 9606
200 6L49 4 D, H, N, R, V, Z Histone H2B type 1-J 9606
201 6L4A 4 D, H, N, R, V, Z Histone H2B type 1-J 9606
202 6UGM 4 D Histone H2B 8355
203 6UGM 5 H Histone H2B 1.1 8355
204 6UH5 4 D Histone H2B 8355
205 6UH5 5 H Histone H2B 8355
206 6KW4 20 P, T Histone H4 8355
207 6KW5 18 U, Y Histone H4 8355
208 6KW3 20 P, T Histone H4 8355
209 6SEG 4 D, H Histone H2B type 1-C/E/F/G/I 9606
210 6SE0 4 D, H Histone H2B type 1-C/E/F/G/I 9606
211 6SE6 4 D, H Histone H2B type 1-C/E/F/G/I 9606
212 6SEE 4 D, H Histone H2B type 1-C/E/F/G/I 9606
213 6SEF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
214 6PX1 4 D, H Histone H2B 1.1 8355
215 6PX3 4 D, H Histone H2B 1.1 8355
216 6PWV 7 J, N Histone H2B 1.1 8355
217 6PWW 7 J, N Histone H2B 1.1 8355
218 6PWX 5 J, N Histone H2B 1.1 8355
219 6KIU 4 D, H Histone H2B 1.1 8355
220 6KIV 4 D, H Histone H2B 1.1 8355
221 6KIW 4 D, H Histone H2B 1.1 8355
222 6KIX 4 D, H Histone H2B 1.1 8355
223 6KIZ 4 D, H Histone H2B 1.1 8355
224 6S01 4 D, H Histone H2B 1.1 8355
225 6RYU 4 D, H Histone H2B 1.1 8355
226 6PA7 4 D, H Histone H2B 1.1 8355
227 6RYR 4 D, H Histone H2B 1.1 8355
228 6K1P 4 D, H Histone H2B 1.1 8355
229 6RNY 4 D, H Histone H2B type 1-C/E/F/G/I 9606
230 6JYL 4 D, H Histone H2B 1.1 8355
231 6R8Y 4 D, H Histone H2B type 1-J 9606
232 6R8Z 4 D, H Histone H2B type 1-J 9606
233 6R90 4 D, H Histone H2B type 1-J 9606
234 6R91 4 D, H Histone H2B type 1-J 9606
235 6R92 7 D, H Histone H2B type 1-J 9606
236 6R93 6 D, H Histone H2B type 1-J 9606
237 6R94 6 D, H Histone H2B type 1-J 9606
238 6R1U 4 D, H Histone H2B 1.1 8355
239 6R25 7 D, H H2B 8355
240 6O96 4 D, H Histone H2B 1.1 8355
241 6R0C 4 D, H Histone H2B type 1-C/E/F/G/I 9606
242 6O1D 4 D, H Histone H2B type 1-J 9606
243 6NZO 4 D, H Histone H2B 1.1 8355
244 6J99 4 D, H Histone H2B 1.1 8355
245 6NQA 5 D, H Histone H2B 1.1 8355
246 6NOG 4 D, H Histone H2B 1.1 8355
247 6NN6 4 D, H Histone H2B 1.1 8355
248 6J4W 22 d, h Histone H2B type 1-J 9606
249 6J4X 22 d, h Histone H2B type 1-J 9606
250 6J4Y 22 d, h Histone H2B type 1-J 9606
251 6J4Z 21 d, h Histone H2B type 1-J 9606
252 6J50 21 d, h Histone H2B type 1-J 9606
253 6J51 22 d, h Histone H2B type 1-J 9606
254 6NJ9 3 D, H Histone H2B 1.1 8355
255 6I84 6 R, W Histone H2B 1.1 8355
256 6IRO 5 D, H Histone H2B 1.1 8355
257 6IR9 22 d, h Histone H2B type 1-J 9606
258 6INQ 19 d, h Histone H2B type 1-J 9606
259 6HTS 8 L, P Histone H2B type 1-J 9606
260 6E0C 4 D, H Histone H2B type 1-J 9606
261 6E0P 4 D, H Histone H2B type 1-J 9606
262 6A5O 19 d, h Histone H2B type 1-J 9606
263 6A5P 19 d, h Histone H2B type 1-J 9606
264 6A5R 19 d, h Histone H2B type 1-J 9606
265 6A5T 19 d, h Histone H2B type 1-J 9606
266 6A5U 19 d, h Histone H2B, Histone H2B type 1-J 9606
267 6A5L 19 d, h Histone H2B type 1-J 9606
268 6G0L 4 D, H Histone H4 8355
269 6FTX 4 D, H Histone H2B 8364
270 6FML 12 P, T Histone H2B type 1-C/E/F/G/I 9606
271 5Z3L 4 D, H Histone H2B 1.1 8355
272 5Z3O 4 D, H Histone H2B 1.1 8355
273 5Z3U 5 D, H Histone H2B 1.1 8355
274 5Z3V 5 D, H Histone H2B 1.1 8355
275 6C0W 4 D, H Histone H2B 9606
276 6BUZ 4 D, H Histone H2B 9606
277 6ESF 4 D, H Histone H2B 1.1 8355
278 6ESG 4 D, H Histone H2B 1.1 8355
279 6ESH 4 D, H Histone H2B 1.1 8355
280 6ESI 4 D Histone H2B 1.1 8355
281 6ESI 5 H Histone H2B 1.1 8355
282 5O9G 4 D Histone H2B 1.1 8355
283 5O9G 5 H Histone H2B 1.1 8355
284 5X0X 4 D, H Histone H2B 1.1 8355
285 5X0Y 4 D, H Histone H2B 1.1 8355
286 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
287 2RVQ 2 D Histone H2B type 1-J 9606
288 3C9K 2 B, F Histone H2B 7 9031