Sequence Similarity Clusters for the Entities in PDB 3AFA

Entity #1 | Chains: A,E
Histone H3.1 protein, length: 139 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 24 70 203
95 % 57 192 71 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.1
PDBFlex
90 % 57 199 71
70 % 59 202 83
50 % 60 206 111
40 % 60 206 131
30 % 60 206 144
Entity #2 | Chains: B,F
Histone H4 protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 61 205 49
95 % 63 208 60 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 64 216 64
70 % 64 216 75
50 % 64 216 104
40 % 64 216 124
30 % 64 216 138
Entity #3 | Chains: C,G
Histone H2A type 1-B/E protein, length: 133 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 22 79 193
95 % 50 189 73 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.5
PDBFlex
90 % 52 198 68
70 % 54 206 78
50 % 60 217 102
40 % 60 217 120
30 % 60 217 131
Entity #4 | Chains: D,H
Histone H2B type 1-J protein, length: 129 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 23 73 205
95 % 23 73 263 Flexibility: No
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 51 184 79
70 % 54 198 87
50 % 54 198 116
40 % 54 198 139
30 % 54 198 152
Entity #5 | Chains: I,J
146-MER DNA dna, length: 146 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name

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 4 D, H HISTONE H4-VI 9031
2 4H9N 2 B Histone H4 9606
3 4H9Q 2 B Histone H4 9606
4 1KX5 4 B, F histone H4 8355
5 4H9O 2 B Histone H4 9606
6 2ARO 4 D, H HISTONE H4-VI 9031
7 5B0Z 2 B, F Histone H4 9606
8 5Y0D 2 B, F Histone H4 9606
9 5Y0C 3 B, F Histone H4 9606
10 4H9R 2 B Histone H4 9606
11 1S32 3 B, F Histone H4 8355
12 4H9P 2 B Histone H4 9606
13 5AV8 2 B, F Histone H4 9606
14 1KX3 3 B, F histone H4 8355
15 5AV9 2 B, F Histone H4 9606
16 5AV6 2 B, F Histone H4 9606
17 1HQ3 4 D, H HISTONE H4-VI 9031
18 5BNX 2 B Histone H4 9606
19 3UTA 2 B, F Histone H4 8355
20 5X7X 2 B, F Histone H4 9606
21 5B31 2 B, F Histone H4 9606
22 5B1L 2 B, F Histone H4 10090
23 3UTB 2 B, F Histone H4 8355
24 1M19 3 B, F Histone H4 8355
25 5AVB 2 B, F Histone H4 9606
26 5AVC 2 B, F Histone H4 9606
27 5AV5 2 B, F Histone H4 9606
28 3C1B 2 B, F Histone H4 8355
29 5B1M 2 B, F Histone H4 10090
30 2NQB 3 B, F Histone H4 7227
31 5JA4 2 B Histone H4 9606
32 5OMX 4 B, F Histone H4 8355
33 5F99 2 B, F Histone H4 8355
34 5Z30 2 B, F Histone H4 9606
35 5JRG 2 B, F Histone H4 9606
36 3UT9 2 B, F Histone H4 8355
37 5B32 2 B, F Histone H4 9606
38 3R45 2 B Histone H4 9606
39 4WU8 4 B, F Histone H4 8355
40 1P3I 3 B, F Histone H4 8355
41 3MGR 2 B, F Histone H4 8355
42 1F66 3 B, F HISTONE H4 10090
43 3AZG 2 B, F Histone H4 9606
44 1M18 3 B, F Histone H4 8355
45 5B2J 2 B, F Histone H4 9606
46 2PYO 4 B, F Histone H4 7227
47 1P3L 3 B, F Histone H4 8355
48 1EQZ 5 D, H PROTEIN (HISTONE H4) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
49 5B0Y 2 B, F Histone H4 9606
50 2CV5 3 B, F Histone H4 9606
51 5CP6 4 B, F Histone H4 8355
52 5ZBX 2 B, F Histone H4 9606
53 5XF6 2 B, F Histone H4 8355
54 3MGP 2 B, F Histone H4 8355
55 3MVD 2 B, F Histone H4 8355
56 4J8U 2 B, F Histone H4 8355
57 4WU9 2 B, F Histone H4 8355
58 2YFW 2 B, D, F, H HISTONE H4 28985
59 3REH 2 B, F Histone H4 8355
60 3AZL 2 B, F Histone H4 9606
61 5Z23 2 B, F Histone H4 9606
62 3NQU 2 B Histone H4 9606
63 5BNV 2 B, E Histone H4 9606
64 3AFA 2 B, F Histone H4 9606
65 5E5A 3 B, F Histone H4 8355
66 3REJ 2 B, F Histone H4 8355
67 3AZF 2 B, F Histone H4 9606
68 5GTC 2 B, F Histone H4 9606
69 1P3P 3 B, F Histone H4 8355
70 3AV1 2 B, F Histone H4 9606
71 1M1A 3 B, F Histone H4 8355
72 5CPK 2 B, F Histone H4 9606
73 5AY8 2 B, F Histone H4 9606
74 3MNN 2 B, F Histone H4 8355
75 5BO0 2 B Histone H4 9606
76 1P3G 3 B, F Histone H4 8355
77 4J8W 2 B, F Histone H4 8355
78 1P34 3 B, F Histone H4 8355
79 5XF3 2 B, F Histone H4 9606
80 3X1V 3 B, F Histone H4 9606
81 5ONG 4 B, F Histone H4 8355
82 5ONW 4 B, F Histone H4 8355
83 5DNM 2 B, F Histone H4 8355
84 4HGA 3 C Histone H4 9606
85 4UUZ 2 B HISTONE H4 7227
86 3MGQ 2 B, F Histone H4 8355
87 3WTP 2 B, F Histone H4 9606
88 3X1T 3 B, F Histone H4 9606
89 2NZD 4 B, F Histone H4 8355
90 3A6N 2 B, F Histone H4 9606
91 5DNN 2 B, F Histone H4 8355
92 5GT3 2 B, F Histone H4 9606
93 5GT0 2 B, F Histone H4 9606
94 3LJA 2 B, F Histone H4 8355
95 3AZI 2 B, F Histone H4 9606
96 3TU4 2 B, F Histone H4 8355
97 1P3O 3 B, F Histone H4 8355
98 4Z2M 3 H, J Histone H4 9606
99 1KX4 3 B, F histone H4 8355
100 3AZN 2 B, F Histone H4 9606
101 1P3M 3 B, F Histone H4 8355
102 4J8V 2 B, F Histone H4 8355
103 5B33 2 B, F Histone H4 9606
104 3X1S 2 B, F Histone H4 9606
105 3LZ0 2 B, F Histone H4 8355
106 1P3F 3 B, F Histone H4 8355
107 1P3K 3 B, F Histone H4 8355
108 4XYI 2 B Histone H4 4897
109 5B2I 2 B, F Histone H4 9606
110 1P3A 3 B, F Histone H4 8355
111 3LZ1 2 B, F Histone H4 8355
112 2IO5 3 C Histone H4 8355
113 5GXQ 2 B, F Histone H4 9606
114 2F8N 3 B, F Histone H4 8355
115 4Z5T 2 B, F Histone H4 9606
116 1U35 3 B, F Hist1h4i protein 10090
117 5XM0 2 B, F Histone H4 10090
118 3AV2 2 B, F Histone H4 9606
119 3AYW 2 B, F Histone H4 9606
120 5XF5 2 B, F Histone H4 9606
121 3AZJ 2 B, F Histone H4 9606
122 3REK 2 B, F Histone H4 8355
123 4KGC 2 B, F Histone H4 8355
124 1ZLA 3 B, F Histone H4 8355
125 5GSU 2 B, F Histone H4 9606
126 5XF4 2 B, F Histone H4 9606
127 3REL 2 B, F Histone H4 8355
128 5GSE 2 B, F, L, P Histone H4 9606
129 3REI 2 B, F Histone H4 8355
130 1P3B 3 B, F Histone H4 8355
131 3WKJ 2 B, F Histone H4 9606
132 4KUD 2 B, F Histone H4 4932
133 3AZK 2 B, F Histone H4 9606
134 4J8X 2 B, F Histone H4 8355
135 3LEL 2 B, F, L, P Histone H4 8355
136 3KUY 2 B, F Histone H4 8355
137 4R8P 2 B, F Histone H4 8355
138 3AZM 2 B, F Histone H4 9606
139 3X1U 3 B, F Histone H4 9606
140 3MGS 2 B, F Histone H4 8355
141 3WA9 2 B, F Histone H4 9606
142 1ID3 3 B, F HISTONE H4 4932
143 3C1C 2 B, F Histone H4 8355
144 3AZH 2 B, F Histone H4 9606
145 5B40 2 B, F Histone H4 9606
146 3WAA 2 B, F Histone H4 9606
147 5CPI 2 B, F Histone H4 9606
148 4JJN 2 B, F Histone H4 4932
149 3AZE 2 B, F Histone H4 9606
150 3W96 2 B, F Histone H4 9606
151 5XM1 2 B, F Histone H4 10090
152 5CPJ 2 B, F Histone H4 9606
153 5B24 2 B, F Histone H4 9606
154 5BS7 2 C, D Histone H4 8355
155 5C3I 3 C, G, K, O, S, W Histone H4 9606
156 2HIO 4 D PROTEIN (HISTONE H4) 9031
157 4QLC 4 B, F Histone H4 7227
158 4LD9 2 B, F Histone H4 8355
159 5ZBB 4 D Histone H4 4932
160 3O62 2 B, F Histone H4 8355
161 4XUJ 2 B, F Histone H4 UNP residues 2-103 8355
162 5KDM 2 B Histone H4 9606
163 3W97 2 B, F Histone H4 9606
164 4YM5 2 B, F Histone H4 9606
165 5ZBA 4 D Histone H4 4932
166 4YM6 2 B, F Histone H4 9606
167 2FJ7 4 B, F Histone H4 8355
168 3W98 2 B, F Histone H4 9606
169 4ZUX 2 B, F, L, P Histone H4 8355
170 3AN2 2 B, F Histone H4 9606
171 5BSA 2 C, D Histone H4 8355
172 3B6F 4 B, F Histone H4 8355
173 5OY7 3 B, F, J, N, R, V, Z, d Histone H4 8355
174 3B6G 4 B, F Histone H4 8355
175 5NL0 2 B, F, L Histone H4 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
176 3KXB 2 B, F Histone H4 8355
177 5HQ2 2 B Histone H4 8355
178 6HKT 2 B, F, L, P, V, Z, b, f, l, p, v, z Histone H4 THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG 9606
179 5OXV 4 B, F, L, P Histone H4 8355
180 1ZBB 4 B, F, b, f Histone H4 8355
181 6NQA 3 B, F Histone H4 8355
182 6NOG 2 B, F Histone H4 8355
183 6NN6 2 B, F Histone H4 8355
184 6J4W 20 b, f Histone H4 9606
185 6J4X 20 b, f Histone H4 9606
186 6J4Y 20 b, f Histone H4 9606
187 6J4Z 19 b, f Histone H4 9606
188 6J50 19 b, f Histone H4 9606
189 6J51 20 b, f Histone H4 9606
190 6NJ9 1 B, F Histone H4 8355
191 6I84 5 O, U Histone H4 8355
192 6IR9 20 b, f Histone H4 9606
193 6HTS 6 J, N Histone H4 9606
194 6A5O 17 b, f Histone H4 9606
195 6A5P 17 b, f Histone H4 9606
196 6A5R 17 b, f Histone H4 9606
197 6A5T 17 b, f Histone H4 9606
198 6A5U 17 b, f Histone H4 9606
199 6A5V 17 b, f Histone H4 9606
200 6A5L 17 b, f Histone H4 9606
201 6GEN 3 C, D Histone H4 4932
202 6GEJ 3 C, D Histone H4 4932
203 6G0L 2 B, F Histone H4 Histone H4 sequence from X. Laevis. The N-terminal region from 1-19 is not resolved. 8355
204 6FTX 2 B, F Histone H4 8355
205 6FML 10 N, R Histone H4 9606
206 6C0W 2 B, F Histone H4 9606
207 6BUZ 2 B, F Histone H4 9606
208 6ESF 2 B, F Histone H4 8355
209 6ESG 2 B, F Histone H4 8355
210 6ESH 2 B, F Histone H4 8355
211 6ESI 2 B, F Histone H4 8355
212 5O9G 2 B, F Histone H4 8355
213 5X0X 2 B, F Histone H4 8355
214 5X0Y 2 B, F Histone H4 8355
215 5KGF 2 B, F Histone H4 cysteine alkylation at position 20 8355
216 3C9K 4 D, H Histone H4 9031