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 3748
95 % 8 14 3221
90 % 9 16 2860
70 % 8 11 4479
50 % 240 318 65
40 % 240 318 86
30 % 240 318 94
Entity #2 | Chains: B,F
Histone H4 protein, length: 103 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 220 299 9
95 % 242 324 17
90 % 249 333 19
70 % 250 332 25
50 % 250 332 58
40 % 250 332 78
30 % 250 332 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 6007
95 % 215 299 19
90 % 198 272 45
70 % 211 290 39
50 % 224 303 69
40 % 224 303 91
30 % 224 303 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 1606
95 % 169 205 75
90 % 217 294 24
70 % 225 305 31
50 % 230 312 67
40 % 230 312 88
30 % 230 312 95
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 38502
95 % 1 3 30652
90 % 1 3 30153
70 % 1 3 26588
50 % 1 3 23321
40 % 1 3 21317
30 % 1 3 20315

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 3 C, G HISTONE H3 9031
2 4H9N 1 A Histone H3.3 9606
3 4H9Q 1 A Histone H3.3 9606
4 1KX5 3 A, E histone H3 8355
5 4H9O 1 A Histone H3.3 9606
6 2ARO 3 C, G HISTONE H3 9031
7 5B0Z 1 A, E Histone H3.2 9606
8 5Y0D 1 A, E Histone H3.1 9606
9 5Y0C 2 A, E Histone H3.1 9606
10 4H9R 1 A Histone H3.3 9606
11 1S32 2 A, E histone H3 8355
12 4H9P 1 A Histone H3.3 9606
13 5AV8 1 A, E Histone H3.1 9606
14 1KX3 2 A, E histone H3 8355
15 5AV9 1 A, E Histone H3.1 9606
16 5AV6 1 A, E Histone H3.1 9606
17 6JOU 1 A, E Histone H3.1 9606
18 1HQ3 3 C, G HISTONE H3 9031
19 3UTA 1 A, E Histone H3.2 8355
20 6KVD 2 A, E Histone H3.1 9606
21 5X7X 1 A, E Histone H3.3 9606
22 5B31 1 A, E Histone H3.1 9606
23 5B1L 1 A, E Histone H3t 10090
24 6K1K 1 A, E Histone H3.1 9606
25 3UTB 1 A, E Histone H3.2 8355
26 1M19 2 A, E Histone H3.2 8355
27 5AVB 1 A, E Histone H3.1 9606
28 5AVC 1 A, E Histone H3.1 9606
29 5AV5 1 A, E Histone H3.1 9606
30 3C1B 1 A, E Histone H3-like 8355
31 5B1M 1 A, E Histone H3.1 10090
32 2NQB 2 A, E Histone H3 7227
33 5OMX 3 A, E Histone H3.2 8355
34 6JR1 1 A, E Histone H3.1 9606
35 5F99 1 A, E Histone H3.2 8355
36 5Z30 1 A, E Histone H3.1 9606
37 5JRG 1 A, E Histone H3.1 9606
38 3UT9 1 A, E Histone H3.2 8355
39 5B32 1 A, E Histone H3.3 9606
40 4WU8 3 A, E Histone H3.2 8355
41 1P3I 2 A, E Histone H3 8355
42 3MGR 1 A, E Histone H3.2 8355
43 1F66 2 A, E HISTONE H3 8355
44 3AZG 1 A, E Histone H3.1 9606
45 4H9S 1 A, B Histone H3.3 9606
46 1M18 2 A, E Histone H3.2 8355
47 5B2J 1 A, E Histone H3.1 9606
48 6V2K 1 A, E Histone H3.1 9606
49 2PYO 3 A, E Histone H3 7227
50 1P3L 2 A, E Histone H3 8355
51 1EQZ 4 C, G PROTEIN (HISTONE H3) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
52 5B0Y 1 A, E Histone H3.2 9606
53 6JR0 1 A, E Histone H3.1 9606
54 2CV5 2 A, E Histone H3.1 9606
55 5CP6 3 A, E Histone H3.2 8355
56 5ZBX 1 A, E Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1 Chimera protein H3CATD, in which amino acid residues 76-113 of human histone H3.1 were replaced by the corresponding amino acid residues 75-114 of human CENP-A. 9606
57 5XF6 1 A, E Histone H3.2 8355
58 3MGP 1 A, E Histone H3.2 8355
59 3MVD 1 A, E Histone H3.2 8355
60 4J8U 1 A, E Histone H3.2 8355
61 4WU9 1 A, E Histone H3.2 8355
62 3REH 1 A, E Histone H3.2 8355
63 3AZL 1 A, E Histone H3.1 9606
64 5Z23 1 A, E Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1 Chimera protein H3CATD, in which amino acid residues 76-113 of human histone H3.1 were replaced by corresponding amino acid residues 75-114 of human CENP-A. 9606
65 3NQU 1 A Histone H3-like centromeric protein A 9606
66 3AFA 1 A, E Histone H3.1 9606
67 5E5A 2 A, E Histone H3.2 8355
68 3REJ 1 A, E Histone H3.2 8355
69 3AZF 1 A, E Histone H3.1 9606
70 5GTC 1 A, E Histone H3.1 9606
71 1P3P 2 A, E Histone H3 8355
72 3AV1 1 A, E Histone H3.2 9606
73 1M1A 2 A, E Histone H3.2 8355
74 5CPK 1 A, E Histone H3.1 9606
75 5AY8 1 A, E H3.Y 9606
76 3MNN 1 A, E Histone H3.2 8355
77 1P3G 2 A, E Histone H3 8355
78 4J8W 1 A, E Histone H3.2 8355
79 1P34 2 A, E Histone H3 8355
80 5XF3 1 A, E Histone H3.1 9606
81 3X1V 2 A, E Histone H3.1 9606
82 5ONG 3 A, E Histone H3.2 8355
83 5ONW 3 A, E Histone H3.2 8355
84 5DNM 1 A, E Histone H3.2 8355
85 4HGA 2 B Histone H3.3 9606
86 4UUZ 1 A HISTONE H3 7227
87 6K1I 1 A, E Histone H3.1 9606
88 3MGQ 1 A, E Histone H3.2 8355
89 3WTP 1 A Histone H3-like centromeric protein A 9606
90 3WTP 5 E Histone H3.3 9606
91 3X1T 2 A, E Histone H3.1 9606
92 2NZD 3 A, E Histone H3 8355
93 3A6N 1 A, E Histone H3.1t 9606
94 5DNN 1 A, E Histone H3.2 8355
95 5GT3 1 A, E Histone H3.1 9606
96 5GT0 1 A, E Histone H3.1 9606
97 3LJA 1 A, E Histone H3.2 8355
98 3AZI 1 A, E Histone H3.1 9606
99 3TU4 1 A, E Histone H3.2 8355
100 1P3O 2 A, E Histone H3 8355
101 1KX4 2 A, E histone H3 8355
102 3AZN 1 A, E Histone H3.1 9606
103 1P3M 2 A, E Histone H3 8355
104 4J8V 1 A, E Histone H3.2 8355
105 5B33 1 A, E Histone H3.3 9606
106 3X1S 1 A, E Histone H3.1 9606
107 3LZ0 1 A, E Histone H3.2 8355
108 1P3F 2 A, E Histone H3 8355
109 1P3K 2 A, E Histone H3 8355
110 5B2I 1 A, E Histone H3.1 9606
111 1P3A 2 A, E Histone H3 8355
112 3LZ1 1 A, E Histone H3.2 8355
113 2IO5 2 B Histone H3.1 8355
114 5GXQ 1 A, E Histone H3.6 9606
115 2F8N 2 A, E Histone H3.1 8355
116 4Z5T 1 A, E Histone H3.3C 9606
117 1U35 2 A, E Histone H3.1 10090
118 5XM0 1 A, E Histone H3.3 10090
119 3AV2 1 A, E Histone H3.3 9606
120 3AYW 1 A, E Histone H3.1 9606
121 5XF5 1 A, E Histone H3.1 9606
122 3AZJ 1 A, E Histone H3.1 9606
123 3REK 1 A, E Histone H3.2 8355
124 4KGC 1 A, E Histone H3.2 8355
125 1ZLA 2 A, E histone H3 8355
126 5GSU 1 A, E Histone H3.1 9606
127 5XF4 1 A, E Histone H3.1 9606
128 3REL 1 A, E Histone H3.2 8355
129 5GSE 1 A, E, K, O Histone H3.1 9606
130 3REI 1 A, E Histone H3.2 8355
131 1P3B 2 A, E Histone H3 8355
132 3WKJ 1 A, E Histone H3.1 9606
133 4KUD 1 A, E Histone H3 4932
134 3AZK 1 A, E Histone H3.1 9606
135 4J8X 1 A, E Histone H3.2 8355
136 3LEL 1 A, E, K, O Histone H3.2 8355
137 3KUY 1 A, E Histone H3.2 8355
138 4R8P 1 A, E Histone H3.2 8355
139 3AZM 1 A, E Histone H3.1 9606
140 3X1U 2 A, E Histone H3.1 9606
141 3MGS 1 A, E Histone H3.2 8355
142 3WA9 1 A, E Histone H3.1 9606
143 1ID3 2 A, E HISTONE H3 4932
144 3C1C 1 A, E Histone H3-like 8355
145 3AZH 1 A, E Histone H3.1 9606
146 5B40 1 A, E Histone H3.2 9606
147 3WAA 1 A, E Histone H3.1 9606
148 5CPI 1 A, E Histone H3.1 9606
149 4JJN 1 A, E Histone H3 4932
150 3W99 1 A, E Histone H3.1 9606
151 3AZE 1 A, E Histone H3.1 9606
152 6LA8 1 A, E, K, O Histone H3.1 9606
153 3W96 1 A, E Histone H3.1 9606
154 6OM3 1 A, E, M, Q Histone H3.2 8355
155 5XM1 1 A, E Histone H3mm7 10090
156 6K1J 1 A, E Histone H3.1 9606
157 5CPJ 1 A, E Histone H3.1 9606
158 6LA9 1 A, E, K, O Histone H3.1 9606
159 5B24 1 A, E Histone H3.1 9606
160 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
161 2HIO 3 C PROTEIN (HISTONE H3) 9031
162 4QLC 3 A, E Histone H3 7227
163 4LD9 1 A, E Histone H3.2 8355
164 5ZBB 3 C Histone H3 4932
165 3O62 1 A, E Histone H3.2 8355
166 6M44 1 A, E, K, O Histone H3.1 9606
167 6KXV 1 A, E Histone H3 5664
168 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
169 5KDM 1 A Histone H3.3 9606
170 3W97 1 A, E Histone H3.1 9606
171 4YM5 1 A, E Histone H3.1 9606
172 5ZBA 3 C Histone H3 4932
173 4YM6 1 A, E Histone H3.1 9606
174 2FJ7 3 A, E histone H3 8355
175 4ZUX 1 A, E, K, O Histone H3.2 8355
176 6M3V 1 A, E, K, O Histone H3.1 9606
177 3AN2 1 A, E Histone H3-like centromeric protein A 9606
178 6VYP 1 A, E, a, e Histone H3 8355
179 3B6F 3 A, E Histone H3.2 8355
180 5OY7 2 A, E, I, M, Q, U, Y, c Histone H3 8355
181 3B6G 3 A, E Histone H3.2 8355
182 5NL0 1 A, E, K Histone H3.2 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
183 3KXB 1 A, E Histone H3.2 8355
184 5HQ2 1 A Histone H3.2 8355
185 6HKT 1 A, E, K, O, U, Y, a, e, k, o, u, y Histone H3.1 THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG 9606
186 5OXV 5 A, E, K, O Histone H3.2 8355
187 1ZBB 3 A, E, a, e HISTONE H3 8355
188 7K63 1 A, E Histone H3.1 9606
189 7K5X 1 A, E Histone H3.1 9606
190 7K5Y 1 A, E Histone H3.1 9606
191 7K60 1 A, E Histone H3.1 9606
192 7K61 1 A, E Histone H3.1 9606
193 7CRO 1 E, M Histone H3 8355
194 7CRP 1 E, M Histone H3 8355
195 7CRQ 1 E, M Histone H3 8355
196 7CRR 1 E, M Histone H3 8355
197 7A08 6 d, h Histone H3.3 9606
198 7JO9 1 A, E Histone H3.2 9606
199 7JOA 1 A, E Histone H3.2 9606
200 6XJD 1 A, E Histone H3.2 9606
201 6X59 1 A, E Histone H3.2 9606
202 6X5A 1 A, E Histone H3.2 9606
203 6X0N 1 A, E, a, e Histone H3.2 8355
204 6WZ5 1 A, E Histone H3.2 8355
205 6WZ9 1 A, E Histone H3.2 8355
206 7C0M 1 A, E, a, e Histone H3.1 9606
207 6YOV 1 A Histone H3.1 9606
208 6YOV 5 E Histone H3.1 9606
209 6M4H 3 A, E Histone H3.1 9606
210 6M4D 1 A, E Histone H3.1 9606
211 6M4G 3 A, E Histone H3.1 9606
212 6LTJ 1 A, E Histone H3.3 8355
213 6VEN 1 A, E Histone H3.2 8355
214 6V92 23 a, e Histone H3.1 9606
215 6TEM 1 A, E Histone H3-like centromeric protein A 9606
216 6TDA 1 A, E Histone H3.2 8355
217 6UXW 1 R, V Histone H3.2 8355
218 6T9L 1 A, E Histone H3.2 8355
219 6USJ 3 A, E, K, O Histone H3.1 9606
220 6T90 1 A Histone H3.1 9606
221 6T90 5 E Histone H3.1 9606
222 6T93 1 A, E Histone H3.1 9606
223 6T79 1 A, E Histone H3.2 9606
224 6T7A 1 A, E Histone H3.2 9606
225 6T7B 1 A, E Histone H3.2 9606
226 6T7C 1 A, E Histone H3.2 9606
227 6T7D 1 A, E Histone H3.2 9606
228 6UPK 1 A, E Histone H3.1 9606
229 6UPL 1 A, E Histone H3.1 9606
230 6L49 1 A, E Histone H3-like centromeric protein A 9606
231 6L49 7 K, O, S, W Histone H3.1 9606
232 6L4A 1 A, E, K, O, S, W Histone H3.1 9606
233 6UGM 1 A, E Histone H3 8355
234 6UH5 1 A, E Histone H3 8355
235 6KW4 1 N, Q Histone H3.2 8355
236 6KW5 16 R, V Histone H3.2 8355
237 6KW3 2 N, Q Histone H3.2 8355
238 6SEG 1 A, E Histone H3-like centromeric protein A 9606
239 6SE0 1 A, E Histone H3-like centromeric protein A 9606
240 6SE6 1 A, E Histone H3-like centromeric protein A 9606
241 6SEE 1 A, E Histone H3-like centromeric protein A 9606
242 6SEF 1 A, E Histone H3-like centromeric protein A 9606
243 6PX1 1 A, E Histone H3 8355
244 6PX3 1 A, E Histone H3 8355
245 6PWV 4 G, K Histone H3.2 8355
246 6PWW 4 G, K Histone H3.2 8355
247 6PWX 2 G, K Histone H3.2 8355
248 6PWE 1 A, E Histone H3 7227
249 6PWF 1 A, E Histone H3 7227
250 6KIU 1 A, E Histone H3 8355
251 6KIV 1 A, E Histone H3 8355
252 6KIW 1 A, E Histone H3 8355
253 6KIX 1 A, E Histone H3 8355
254 6KIZ 1 A, E Histone H3 8355
255 6S01 1 A, E Histone H3 residue K36 was chemically modified to be ML3. 8355
256 6RYU 1 A, E Histone H3.2 8355
257 6PA7 1 A, E Histone H3.2 8355
258 6RYR 1 A, E Histone H3.2 8355
259 6K1P 1 A, E Histone H3 8355
260 6RNY 1 A, E Histone H3.3 9606
261 6JYL 1 A, E Histone H3 8355
262 6R8Y 1 A, E Histone H3.1 9606
263 6R8Z 1 A, E Histone H3.1 9606
264 6R90 1 A, E Histone H3.1 9606
265 6R91 1 A, E Histone H3.1 9606
266 6R92 4 A, E Histone H3.1 9606
267 6R93 3 A, E Histone H3.1 9606
268 6R94 3 A, E Histone H3.1 9606
269 6R1U 1 A, E Histone H3.2 8355
270 6R1U 9 M Histone H3 8355
271 6R25 3 M Histone H3 8355
272 6R25 4 A, E Histone H3 8355
273 6O96 1 A, E Histone H3.2 8355
274 6R0C 1 A, E Histone H3.3 9606
275 6O22 4 E Histone H3.2 8355
276 6NZO 1 A, E Histone H3 8355
277 6J99 1 A, E Histone H3 8355
278 6NQA 8 A, E Histone H3.2 8355
279 6NOG 1 A, E Histone H3.2 8355
280 6NN6 1 A, E Histone H3.2 8355
281 6J4W 19 a, e Histone H3.3 9606
282 6J4X 19 a, e Histone H3.3 9606
283 6J4Y 19 a, e Histone H3.3 9606
284 6J4Z 18 a, e Histone H3.3 9606
285 6J50 18 a, e Histone H3.3 9606
286 6J51 19 a, e Histone H3.3 9606
287 6NJ9 6 A, E Histone H3.2 8355
288 6NE3 1 A, E Histone H3.2 8355
289 6I84 1 M, S Histone H3.2 8355
290 6IRO 2 A, E Histone H3 8355
291 6IR9 19 a, e Histone H3.3 9606
292 6INQ 16 a, e Histone H3.3 9606
293 6HTS 5 I, M Histone H3.1 9606
294 6DZT 1 A, E Histone H3 7227
295 6A5O 16 a, e Histone H3.3 9606
296 6A5P 16 a, e Histone H3.3 9606
297 6A5R 16 a, e Histone H3.3 9606
298 6A5T 16 a, e Histone H3.3 9606
299 6A5U 16 a, e Histone H3.3 9606
300 6A5L 16 a, e Histone H3.3 9606
301 6GEN 2 A, B Histone H3 4932
302 6GEJ 2 A, B Histone H3 4932
303 6G0L 1 A, E Histone H3 Histone H3 sequence from X. Laevis. The N-terminal region from 1-39 is not resolved. 8355
304 6FML 9 M, Q Histone H3.2 9606
305 5Z3L 1 A, E Histone H3.2 8355
306 5Z3O 1 A, E Histone H3.2 8355
307 5Z3U 2 A, E Histone H3.2 8355
308 5Z3V 2 A, E Histone H3.2 8355
309 6C0W 1 A, E Histone H3-like centromeric protein A 9606
310 6ESF 1 A, E Histone H3.2 8355
311 6ESG 1 A, E Histone H3.2 8355
312 6ESH 1 A, E Histone H3.2 8355
313 6ESI 1 A, E Histone H3.2 8355
314 5O9G 1 A, E Histone H3.2 8355
315 5X0X 1 A, E Histone H3.2 8355
316 5X0Y 1 A, E Histone H3.2 8355
317 5KGF 1 A, E Histone H3.2 8355
318 3C9K 3 C, G Histone H3.2 9031