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 69 200
95 % 57 180 71 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.1
PDBFlex
90 % 57 187 75
70 % 57 188 85
50 % 58 192 114
40 % 58 192 138
30 % 58 192 150
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 % 59 191 51
95 % 61 194 63 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 62 202 68
70 % 62 202 82
50 % 62 202 109
40 % 62 202 131
30 % 62 202 143
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 % 21 71 205
95 % 49 176 72 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.5
PDBFlex
90 % 51 185 71
70 % 53 193 83
50 % 59 204 105
40 % 59 204 125
30 % 59 204 136
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 % 21 64 230
95 % 49 170 77 Flexibility: No
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 49 170 82
70 % 52 184 91
50 % 52 184 124
40 % 52 184 142
30 % 52 184 154
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 5XF6 2 B, F Histone H4 8355
53 3MGP 2 B, F Histone H4 8355
54 3MVD 2 B, F Histone H4 8355
55 4J8U 2 B, F Histone H4 8355
56 4WU9 2 B, F Histone H4 8355
57 2YFW 2 B, D, F, H HISTONE H4 28985
58 3REH 2 B, F Histone H4 8355
59 3AZL 2 B, F Histone H4 9606
60 3NQU 2 B Histone H4 9606
61 5BNV 2 B, E Histone H4 9606
62 3AFA 2 B, F Histone H4 9606
63 5E5A 3 B, F Histone H4 8355
64 3REJ 2 B, F Histone H4 8355
65 3AZF 2 B, F Histone H4 9606
66 5GTC 2 B, F Histone H4 9606
67 1P3P 3 B, F Histone H4 8355
68 3AV1 2 B, F Histone H4 9606
69 1M1A 3 B, F Histone H4 8355
70 5CPK 2 B, F Histone H4 9606
71 5AY8 2 B, F Histone H4 9606
72 3MNN 2 B, F Histone H4 8355
73 5BO0 2 B Histone H4 9606
74 1P3G 3 B, F Histone H4 8355
75 4J8W 2 B, F Histone H4 8355
76 1P34 3 B, F Histone H4 8355
77 5XF3 2 B, F Histone H4 9606
78 3X1V 3 B, F Histone H4 9606
79 5ONG 4 B, F Histone H4 8355
80 5ONW 4 B, F Histone H4 8355
81 5DNM 2 B, F Histone H4 8355
82 4HGA 3 C Histone H4 9606
83 4UUZ 2 B HISTONE H4 7227
84 3MGQ 2 B, F Histone H4 8355
85 3WTP 2 B, F Histone H4 9606
86 3X1T 3 B, F Histone H4 9606
87 2NZD 4 B, F Histone H4 8355
88 3A6N 2 B, F Histone H4 9606
89 5DNN 2 B, F Histone H4 8355
90 5GT3 2 B, F Histone H4 9606
91 5GT0 2 B, F Histone H4 9606
92 3LJA 2 B, F Histone H4 8355
93 3AZI 2 B, F Histone H4 9606
94 3TU4 2 B, F Histone H4 8355
95 1P3O 3 B, F Histone H4 8355
96 4Z2M 3 H, J Histone H4 9606
97 1KX4 3 B, F histone H4 8355
98 3AZN 2 B, F Histone H4 9606
99 1P3M 3 B, F Histone H4 8355
100 4J8V 2 B, F Histone H4 8355
101 5B33 2 B, F Histone H4 9606
102 3X1S 2 B, F Histone H4 9606
103 3LZ0 2 B, F Histone H4 8355
104 1P3F 3 B, F Histone H4 8355
105 1P3K 3 B, F Histone H4 8355
106 4XYI 2 B Histone H4 4897
107 5B2I 2 B, F Histone H4 9606
108 1P3A 3 B, F Histone H4 8355
109 3LZ1 2 B, F Histone H4 8355
110 2IO5 3 C Histone H4 8355
111 5GXQ 2 B, F Histone H4 9606
112 2F8N 3 B, F Histone H4 8355
113 4Z5T 2 B, F Histone H4 9606
114 1U35 3 B, F Hist1h4i protein 10090
115 5XM0 2 B, F Histone H4 10090
116 3AV2 2 B, F Histone H4 9606
117 3AYW 2 B, F Histone H4 9606
118 5XF5 2 B, F Histone H4 9606
119 3AZJ 2 B, F Histone H4 9606
120 3REK 2 B, F Histone H4 8355
121 4KGC 2 B, F Histone H4 8355
122 1ZLA 3 B, F Histone H4 8355
123 5GSU 2 B, F Histone H4 9606
124 5XF4 2 B, F Histone H4 9606
125 3REL 2 B, F Histone H4 8355
126 5GSE 2 B, F, L, P Histone H4 9606
127 3REI 2 B, F Histone H4 8355
128 1P3B 3 B, F Histone H4 8355
129 3WKJ 2 B, F Histone H4 9606
130 4KUD 2 B, F Histone H4 4932
131 3AZK 2 B, F Histone H4 9606
132 4J8X 2 B, F Histone H4 8355
133 3LEL 2 B, F, L, P Histone H4 8355
134 3KUY 2 B, F Histone H4 8355
135 4R8P 2 B, F Histone H4 8355
136 3AZM 2 B, F Histone H4 9606
137 3X1U 3 B, F Histone H4 9606
138 3MGS 2 B, F Histone H4 8355
139 3WA9 2 B, F Histone H4 9606
140 1ID3 3 B, F HISTONE H4 4932
141 3C1C 2 B, F Histone H4 8355
142 3AZH 2 B, F Histone H4 9606
143 5B40 2 B, F Histone H4 9606
144 3WAA 2 B, F Histone H4 9606
145 5CPI 2 B, F Histone H4 9606
146 4JJN 2 B, F Histone H4 4932
147 3AZE 2 B, F Histone H4 9606
148 3W96 2 B, F Histone H4 9606
149 5XM1 2 B, F Histone H4 10090
150 5CPJ 2 B, F Histone H4 9606
151 5B24 2 B, F Histone H4 9606
152 5BS7 2 C, D Histone H4 8355
153 5C3I 3 C, G, K, O, S, W Histone H4 9606
154 2HIO 4 D PROTEIN (HISTONE H4) 9031
155 4QLC 4 B, F Histone H4 7227
156 4LD9 2 B, F Histone H4 8355
157 5ZBB 4 D Histone H4 4932
158 3O62 2 B, F Histone H4 8355
159 4XUJ 2 B, F Histone H4 UNP residues 2-103 8355
160 5KDM 2 B Histone H4 9606
161 3W97 2 B, F Histone H4 9606
162 4YM5 2 B, F Histone H4 9606
163 5ZBA 4 D Histone H4 4932
164 4YM6 2 B, F Histone H4 9606
165 2FJ7 4 B, F Histone H4 8355
166 3W98 2 B, F Histone H4 9606
167 4ZUX 2 B, F, L, P Histone H4 8355
168 3AN2 2 B, F Histone H4 9606
169 5BSA 2 C, D Histone H4 8355
170 3B6F 4 B, F Histone H4 8355
171 5OY7 3 B, F, J, N, R, V, Z, d Histone H4 8355
172 3B6G 4 B, F Histone H4 8355
173 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
174 3KXB 2 B, F Histone H4 8355
175 5HQ2 2 B Histone H4 8355
176 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
177 5OXV 4 B, F, L, P Histone H4 8355
178 1ZBB 4 B, F, b, f Histone H4 8355
179 6HTS 6 J, N Histone H4 9606
180 6A5O 17 b, f Histone H4 9606
181 6A5P 17 b, f Histone H4 9606
182 6A5R 17 b, f Histone H4 9606
183 6A5T 17 b, f Histone H4 9606
184 6A5U 17 b, f Histone H4 9606
185 6A5V 17 b, f Histone H4 9606
186 6A5L 17 b, f Histone H4 9606
187 6GEN 3 C, D Histone H4 4932
188 6GEJ 3 C, D Histone H4 4932
189 6G0L 2 B, F Histone H4 Histone H4 sequence from X. Laevis. The N-terminal region from 1-19 is not resolved. 8355
190 6FTX 2 B, F Histone H4 8355
191 6FML 10 N, R Histone H4 9606
192 6C0W 2 B, F Histone H4 9606
193 6BUZ 2 B, F Histone H4 9606
194 6ESF 2 B, F Histone H4 8355
195 6ESG 2 B, F Histone H4 8355
196 6ESH 2 B, F Histone H4 8355
197 6ESI 2 B, F Histone H4 8355
198 5O9G 2 B, F Histone H4 8355
199 5X0X 2 B, F Histone H4 8355
200 5X0Y 2 B, F Histone H4 8355
201 5KGF 2 B, F Histone H4 cysteine alkylation at position 20 8355
202 3C9K 4 D, H Histone H4 9031