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 3380
95 % 8 14 3017
90 % 9 16 2683
70 % 8 11 4184
50 % 211 289 81
40 % 211 289 97
30 % 211 289 97
Entity #2 | Chains: B,F
Histone H4 protein, length: 103 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 190 269 20
95 % 212 294 26
90 % 219 303 20
70 % 220 302 33
50 % 220 302 74
40 % 220 302 91
30 % 220 302 93
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 9144
95 % 184 268 38
90 % 171 245 66
70 % 184 263 53
50 % 197 276 84
40 % 197 276 103
30 % 197 276 101
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 % 6 13 2483
95 % 147 183 84
90 % 187 264 45
70 % 195 275 51
50 % 200 282 83
40 % 200 282 101
30 % 200 282 100
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 35354
95 % 1 3 29205
90 % 1 3 28133
70 % 1 3 25464
50 % 1 3 22286
40 % 1 3 20375
30 % 1 3 18247

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 2PYO 3 A, E Histone H3 7227
49 1P3L 2 A, E Histone H3 8355
50 1EQZ 4 C, G PROTEIN (HISTONE H3) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
51 5B0Y 1 A, E Histone H3.2 9606
52 6JR0 1 A, E Histone H3.1 9606
53 2CV5 2 A, E Histone H3.1 9606
54 5CP6 3 A, E Histone H3.2 8355
55 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
56 5XF6 1 A, E Histone H3.2 8355
57 3MGP 1 A, E Histone H3.2 8355
58 3MVD 1 A, E Histone H3.2 8355
59 4J8U 1 A, E Histone H3.2 8355
60 4WU9 1 A, E Histone H3.2 8355
61 3REH 1 A, E Histone H3.2 8355
62 3AZL 1 A, E Histone H3.1 9606
63 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
64 3NQU 1 A Histone H3-like centromeric protein A 9606
65 3AFA 1 A, E Histone H3.1 9606
66 5E5A 2 A, E Histone H3.2 8355
67 3REJ 1 A, E Histone H3.2 8355
68 3AZF 1 A, E Histone H3.1 9606
69 5GTC 1 A, E Histone H3.1 9606
70 1P3P 2 A, E Histone H3 8355
71 3AV1 1 A, E Histone H3.2 9606
72 1M1A 2 A, E Histone H3.2 8355
73 5CPK 1 A, E Histone H3.1 9606
74 5AY8 1 A, E H3.Y 9606
75 3MNN 1 A, E Histone H3.2 8355
76 1P3G 2 A, E Histone H3 8355
77 4J8W 1 A, E Histone H3.2 8355
78 1P34 2 A, E Histone H3 8355
79 5XF3 1 A, E Histone H3.1 9606
80 3X1V 2 A, E Histone H3.1 9606
81 5ONG 3 A, E Histone H3.2 8355
82 5ONW 3 A, E Histone H3.2 8355
83 5DNM 1 A, E Histone H3.2 8355
84 4HGA 2 B Histone H3.3 9606
85 4UUZ 1 A HISTONE H3 7227
86 6K1I 1 A, E Histone H3.1 9606
87 3MGQ 1 A, E Histone H3.2 8355
88 3WTP 1 A Histone H3-like centromeric protein A 9606
89 3WTP 5 E Histone H3.3 9606
90 3X1T 2 A, E Histone H3.1 9606
91 2NZD 3 A, E Histone H3 8355
92 3A6N 1 A, E Histone H3.1t 9606
93 5DNN 1 A, E Histone H3.2 8355
94 5GT3 1 A, E Histone H3.1 9606
95 5GT0 1 A, E Histone H3.1 9606
96 3LJA 1 A, E Histone H3.2 8355
97 3AZI 1 A, E Histone H3.1 9606
98 3TU4 1 A, E Histone H3.2 8355
99 1P3O 2 A, E Histone H3 8355
100 1KX4 2 A, E histone H3 8355
101 3AZN 1 A, E Histone H3.1 9606
102 1P3M 2 A, E Histone H3 8355
103 4J8V 1 A, E Histone H3.2 8355
104 5B33 1 A, E Histone H3.3 9606
105 3X1S 1 A, E Histone H3.1 9606
106 3LZ0 1 A, E Histone H3.2 8355
107 1P3F 2 A, E Histone H3 8355
108 1P3K 2 A, E Histone H3 8355
109 5B2I 1 A, E Histone H3.1 9606
110 1P3A 2 A, E Histone H3 8355
111 3LZ1 1 A, E Histone H3.2 8355
112 2IO5 2 B Histone H3.1 8355
113 5GXQ 1 A, E Histone H3.6 9606
114 2F8N 2 A, E Histone H3.1 8355
115 4Z5T 1 A, E Histone H3.3C 9606
116 1U35 2 A, E Histone H3.1 10090
117 5XM0 1 A, E Histone H3.3 10090
118 3AV2 1 A, E Histone H3.3 9606
119 3AYW 1 A, E Histone H3.1 9606
120 5XF5 1 A, E Histone H3.1 9606
121 3AZJ 1 A, E Histone H3.1 9606
122 3REK 1 A, E Histone H3.2 8355
123 4KGC 1 A, E Histone H3.2 8355
124 1ZLA 2 A, E histone H3 8355
125 5GSU 1 A, E Histone H3.1 9606
126 5XF4 1 A, E Histone H3.1 9606
127 3REL 1 A, E Histone H3.2 8355
128 5GSE 1 A, E, K, O Histone H3.1 9606
129 3REI 1 A, E Histone H3.2 8355
130 1P3B 2 A, E Histone H3 8355
131 3WKJ 1 A, E Histone H3.1 9606
132 4KUD 1 A, E Histone H3 4932
133 3AZK 1 A, E Histone H3.1 9606
134 4J8X 1 A, E Histone H3.2 8355
135 3LEL 1 A, E, K, O Histone H3.2 8355
136 3KUY 1 A, E Histone H3.2 8355
137 4R8P 1 A, E Histone H3.2 8355
138 3AZM 1 A, E Histone H3.1 9606
139 3X1U 2 A, E Histone H3.1 9606
140 3MGS 1 A, E Histone H3.2 8355
141 3WA9 1 A, E Histone H3.1 9606
142 1ID3 2 A, E HISTONE H3 4932
143 3C1C 1 A, E Histone H3-like 8355
144 3AZH 1 A, E Histone H3.1 9606
145 5B40 1 A, E Histone H3.2 9606
146 3WAA 1 A, E Histone H3.1 9606
147 5CPI 1 A, E Histone H3.1 9606
148 4JJN 1 A, E Histone H3 4932
149 3W99 1 A, E Histone H3.1 9606
150 3AZE 1 A, E Histone H3.1 9606
151 3W96 1 A, E Histone H3.1 9606
152 6OM3 1 A, E, M, Q Histone H3.2 8355
153 5XM1 1 A, E Histone H3mm7 10090
154 6K1J 1 A, E Histone H3.1 9606
155 5CPJ 1 A, E Histone H3.1 9606
156 5B24 1 A, E Histone H3.1 9606
157 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
158 2HIO 3 C PROTEIN (HISTONE H3) 9031
159 4QLC 3 A, E Histone H3 7227
160 4LD9 1 A, E Histone H3.2 8355
161 5ZBB 3 C Histone H3 4932
162 3O62 1 A, E Histone H3.2 8355
163 6KXV 1 A, E Histone H3 5664
164 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
165 5KDM 1 A Histone H3.3 9606
166 3W97 1 A, E Histone H3.1 9606
167 4YM5 1 A, E Histone H3.1 9606
168 5ZBA 3 C Histone H3 4932
169 4YM6 1 A, E Histone H3.1 9606
170 2FJ7 3 A, E histone H3 8355
171 4ZUX 1 A, E, K, O Histone H3.2 8355
172 3AN2 1 A, E Histone H3-like centromeric protein A 9606
173 6VYP 1 A, E, a, e Histone H3 8355
174 3B6F 3 A, E Histone H3.2 8355
175 5OY7 2 A, E, I, M, Q, U, Y, c Histone H3 8355
176 3B6G 3 A, E Histone H3.2 8355
177 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
178 3KXB 1 A, E Histone H3.2 8355
179 5HQ2 1 A Histone H3.2 8355
180 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
181 5OXV 5 A, E, K, O Histone H3.2 8355
182 1ZBB 3 A, E, a, e HISTONE H3 8355
183 6YOV 1 A Histone H3.1 9606
184 6YOV 5 E Histone H3.1 9606
185 6LTJ 1 A, E Histone H3.3 8355
186 6VEN 1 A, E Histone H3.2 8355
187 6V92 23 a, e Histone H3.1 9606
188 6TEM 1 A, E Histone H3-like centromeric protein A 9606
189 6TDA 1 A, E Histone H3.2 8355
190 6UXW 1 R, V Histone H3.2 8355
191 6T9L 1 A, E Histone H3.2 8355
192 6T90 1 A Histone H3.1 9606
193 6T90 5 E Histone H3.1 9606
194 6T93 1 A, E Histone H3.1 9606
195 6T79 1 A, E Histone H3.2 9606
196 6T7A 1 A, E Histone H3.2 9606
197 6T7B 1 A, E Histone H3.2 9606
198 6T7C 1 A, E Histone H3.2 9606
199 6T7D 1 A, E Histone H3.2 9606
200 6UPK 1 A, E Histone H3.1 9606
201 6UPL 1 A, E Histone H3.1 9606
202 6L49 1 A, E Histone H3-like centromeric protein A 9606
203 6L49 7 K, O, S, W Histone H3.1 9606
204 6L4A 1 A, E, K, O, S, W Histone H3.1 9606
205 6UGM 1 A, E Histone H3 8355
206 6UH5 1 A, E Histone H3 8355
207 6KW4 1 N, Q Histone H3.2 8355
208 6KW3 2 N, Q Histone H3.2 8355
209 6SEG 1 A, E Histone H3-like centromeric protein A 9606
210 6SE0 1 A, E Histone H3-like centromeric protein A 9606
211 6SE6 1 A, E Histone H3-like centromeric protein A 9606
212 6SEE 1 A, E Histone H3-like centromeric protein A 9606
213 6SEF 1 A, E Histone H3-like centromeric protein A 9606
214 6PX1 1 A, E Histone H3 8355
215 6PX3 1 A, E Histone H3 8355
216 6PWV 4 G, K Histone H3.2 8355
217 6PWW 4 G, K Histone H3.2 8355
218 6PWX 2 G, K Histone H3.2 8355
219 6PWE 1 A, E Histone H3 7227
220 6PWF 1 A, E Histone H3 7227
221 6KIU 1 A, E Histone H3 8355
222 6KIV 1 A, E Histone H3 8355
223 6KIW 1 A, E Histone H3 8355
224 6KIX 1 A, E Histone H3 8355
225 6KIZ 1 A, E Histone H3 8355
226 6S01 1 A, E Histone H3 residue K36 was chemically modified to be ML3. 8355
227 6RYU 1 A, E Histone H3.2 8355
228 6PA7 1 A, E Histone H3.2 8355
229 6RYR 1 A, E Histone H3.2 8355
230 6K1P 1 A, E Histone H3 8355
231 6RNY 1 A, E Histone H3.3 9606
232 6JYL 1 A, E Histone H3 8355
233 6R8Y 1 A, E Histone H3.1 9606
234 6R8Z 1 A, E Histone H3.1 9606
235 6R90 1 A, E Histone H3.1 9606
236 6R91 1 A, E Histone H3.1 9606
237 6R92 4 A, E Histone H3.1 9606
238 6R93 3 A, E Histone H3.1 9606
239 6R94 3 A, E Histone H3.1 9606
240 6R1U 1 A, E Histone H3.2 8355
241 6R1U 9 M Histone H3 8355
242 6R25 3 M Histone H3 8355
243 6R25 4 A, E Histone H3 8355
244 6O96 1 A, E Histone H3.2 8355
245 6R0C 1 A, E Histone H3.3 9606
246 6O22 4 E Histone H3.2 8355
247 6NZO 1 A, E Histone H3 8355
248 6J99 1 A, E Histone H3 8355
249 6NQA 8 A, E Histone H3.2 8355
250 6NOG 1 A, E Histone H3.2 8355
251 6NN6 1 A, E Histone H3.2 8355
252 6J4W 19 a, e Histone H3.3 9606
253 6J4X 19 a, e Histone H3.3 9606
254 6J4Y 19 a, e Histone H3.3 9606
255 6J4Z 18 a, e Histone H3.3 9606
256 6J50 18 a, e Histone H3.3 9606
257 6J51 19 a, e Histone H3.3 9606
258 6NJ9 6 A, E Histone H3.2 8355
259 6NE3 1 A, E Histone H3.2 8355
260 6I84 1 M, S Histone H3.2 8355
261 6IRO 2 A, E Histone H3 8355
262 6IR9 19 a, e Histone H3.3 9606
263 6INQ 16 a, e Histone H3.3 9606
264 6HTS 5 I, M Histone H3.1 9606
265 6DZT 1 A, E Histone H3 7227
266 6A5O 16 a, e Histone H3.3 9606
267 6A5P 16 a, e Histone H3.3 9606
268 6A5R 16 a, e Histone H3.3 9606
269 6A5T 16 a, e Histone H3.3 9606
270 6A5U 16 a, e Histone H3.3 9606
271 6A5L 16 a, e Histone H3.3 9606
272 6GEN 2 A, B Histone H3 4932
273 6GEJ 2 A, B Histone H3 4932
274 6G0L 1 A, E Histone H3 Histone H3 sequence from X. Laevis. The N-terminal region from 1-39 is not resolved. 8355
275 6FML 9 M, Q Histone H3.2 9606
276 5Z3L 1 A, E Histone H3.2 8355
277 5Z3O 1 A, E Histone H3.2 8355
278 5Z3U 2 A, E Histone H3.2 8355
279 5Z3V 2 A, E Histone H3.2 8355
280 6C0W 1 A, E Histone H3-like centromeric protein A 9606
281 6ESF 1 A, E Histone H3.2 8355
282 6ESG 1 A, E Histone H3.2 8355
283 6ESH 1 A, E Histone H3.2 8355
284 6ESI 1 A, E Histone H3.2 8355
285 5O9G 1 A, E Histone H3.2 8355
286 5X0X 1 A, E Histone H3.2 8355
287 5X0Y 1 A, E Histone H3.2 8355
288 5KGF 1 A, E Histone H3.2 8355
289 3C9K 3 C, G Histone H3.2 9031