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 % 13 46 326
95 % 54 168 76 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 54 171 77
70 % 54 172 92
50 % 55 176 122
40 % 55 176 142
30 % 55 176 149
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 % 53 161 55
95 % 58 180 68 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 59 185 68
70 % 59 185 83
50 % 59 185 113
40 % 59 185 138
30 % 59 185 143
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 % 19 61 242
95 % 47 163 78 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.6
PDBFlex
90 % 49 171 74
70 % 51 177 87
50 % 56 187 107
40 % 56 187 130
30 % 56 187 138
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 % 16 54 277
95 % 46 157 87 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 46 162 84
70 % 49 169 98
50 % 49 169 132
40 % 49 169 148
30 % 49 169 159
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 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 4H9R 1 A Histone H3.3 9606
9 1S32 2 A, E histone H3 8355
10 4H9P 1 A Histone H3.3 9606
11 5AV8 1 A, E Histone H3.1 9606
12 1KX3 2 A, E histone H3 8355
13 5AV9 1 A, E Histone H3.1 9606
14 5AV6 1 A, E Histone H3.1 9606
15 1HQ3 3 C, G HISTONE H3 9031
16 3UTA 1 A, E Histone H3.2 8355
17 5X7X 1 A, E Histone H3.3 9606
18 5B31 1 A, E Histone H3.1 9606
19 5B1L 1 A, E Histone H3t 10090
20 3UTB 1 A, E Histone H3.2 8355
21 1M19 2 A, E Histone H3.2 8355
22 5AVB 1 A, E Histone H3.1 9606
23 5AVC 1 A, E Histone H3.1 9606
24 5AV5 1 A, E Histone H3.1 9606
25 3C1B 1 A, E Histone H3-like 8355
26 5B1M 1 A, E Histone H3.1 10090
27 2NQB 2 A, E Histone H3 7227
28 5OMX 3 A, E Histone H3.2 8355
29 5F99 1 A, E Histone H3.2 8355
30 5JRG 1 A, E Histone H3.1 9606
31 3UT9 1 A, E Histone H3.2 8355
32 5B32 1 A, E Histone H3.3 9606
33 4WU8 3 A, E Histone H3.2 8355
34 1P3I 2 A, E Histone H3 8355
35 3MGR 1 A, E Histone H3.2 8355
36 1F66 2 A, E HISTONE H3 8355
37 3AZG 1 A, E Histone H3.1 9606
38 4H9S 1 A, B Histone H3.3 9606
39 1M18 2 A, E Histone H3.2 8355
40 5B2J 1 A, E Histone H3.1 9606
41 2PYO 3 A, E Histone H3 7227
42 1P3L 2 A, E Histone H3 8355
43 1EQZ 4 C, G PROTEIN (HISTONE H3) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
44 5B0Y 1 A, E Histone H3.2 9606
45 2CV5 2 A, E Histone H3.1 9606
46 5CP6 3 A, E Histone H3.2 8355
47 5XF6 1 A, E Histone H3.2 8355
48 3MGP 1 A, E Histone H3.2 8355
49 3MVD 1 A, E Histone H3.2 8355
50 4J8U 1 A, E Histone H3.2 8355
51 4WU9 1 A, E Histone H3.2 8355
52 3REH 1 A, E Histone H3.2 8355
53 3AZL 1 A, E Histone H3.1 9606
54 3NQU 1 A Histone H3-like centromeric protein A 9606
55 3AFA 1 A, E Histone H3.1 9606
56 5E5A 2 A, E Histone H3.2 8355
57 3REJ 1 A, E Histone H3.2 8355
58 3AZF 1 A, E Histone H3.1 9606
59 5GTC 1 A, E Histone H3.1 9606
60 1P3P 2 A, E Histone H3 8355
61 3AV1 1 A, E Histone H3.2 9606
62 1M1A 2 A, E Histone H3.2 8355
63 5CPK 1 A, E Histone H3.1 9606
64 5AY8 1 A, E H3.Y 9606
65 3MNN 1 A, E Histone H3.2 8355
66 1P3G 2 A, E Histone H3 8355
67 4J8W 1 A, E Histone H3.2 8355
68 1P34 2 A, E Histone H3 8355
69 5XF3 1 A, E Histone H3.1 9606
70 3X1V 2 A, E Histone H3.1 9606
71 5ONG 3 A, E Histone H3.2 8355
72 5ONW 3 A, E Histone H3.2 8355
73 5DNM 1 A, E Histone H3.2 8355
74 4HGA 2 B Histone H3.3 9606
75 4UUZ 1 A HISTONE H3 7227
76 3MGQ 1 A, E Histone H3.2 8355
77 3WTP 1 A Histone H3-like centromeric protein A 9606
78 3WTP 5 E Histone H3.3 9606
79 3X1T 2 A, E Histone H3.1 9606
80 2NZD 3 A, E Histone H3 8355
81 3A6N 1 A, E Histone H3.1t 9606 2.1.1.64 | Details
82 5DNN 1 A, E Histone H3.2 8355
83 5GT3 1 A, E Histone H3.1 9606
84 5GT0 1 A, E Histone H3.1 9606
85 3LJA 1 A, E Histone H3.2 8355
86 3AZI 1 A, E Histone H3.1 9606
87 3TU4 1 A, E Histone H3.2 8355
88 1P3O 2 A, E Histone H3 8355
89 1KX4 2 A, E histone H3 8355
90 3AZN 1 A, E Histone H3.1 9606
91 1P3M 2 A, E Histone H3 8355
92 4J8V 1 A, E Histone H3.2 8355
93 5B33 1 A, E Histone H3.3 9606
94 3X1S 1 A, E Histone H3.1 9606
95 3LZ0 1 A, E Histone H3.2 8355
96 1P3F 2 A, E Histone H3 8355
97 1P3K 2 A, E Histone H3 8355
98 5B2I 1 A, E Histone H3.1 9606
99 1P3A 2 A, E Histone H3 8355
100 3LZ1 1 A, E Histone H3.2 8355
101 2IO5 2 B Histone H3.1 8355
102 5GXQ 1 A, E Histone H3.6 9606
103 2F8N 2 A, E Histone H3.1 8355
104 4Z5T 1 A, E Histone H3.3C 9606
105 1U35 2 A, E Histone H3.1 10090
106 5XM0 1 A, E Histone H3.3 10090
107 3AV2 1 A, E Histone H3.3 9606
108 3AYW 1 A, E Histone H3.1 9606
109 5XF5 1 A, E Histone H3.1 9606
110 3AZJ 1 A, E Histone H3.1 9606
111 3REK 1 A, E Histone H3.2 8355
112 4KGC 1 A, E Histone H3.2 8355
113 1ZLA 2 A, E histone H3 8355
114 5GSU 1 A, E Histone H3.1 9606
115 5XF4 1 A, E Histone H3.1 9606
116 3REL 1 A, E Histone H3.2 8355
117 5GSE 1 A, E, K, O Histone H3.1 9606
118 3REI 1 A, E Histone H3.2 8355
119 1P3B 2 A, E Histone H3 8355
120 3WKJ 1 A, E Histone H3.1 9606
121 4KUD 1 A, E Histone H3 4932
122 3AZK 1 A, E Histone H3.1 9606
123 4J8X 1 A, E Histone H3.2 8355
124 3LEL 1 A, E, K, O Histone H3.2 8355
125 3KUY 1 A, E Histone H3.2 8355
126 4R8P 1 A, E Histone H3.2 8355
127 3AZM 1 A, E Histone H3.1 9606
128 3X1U 2 A, E Histone H3.1 9606
129 3MGS 1 A, E Histone H3.2 8355
130 3WA9 1 A, E Histone H3.1 9606
131 1ID3 2 A, E HISTONE H3 4932
132 3C1C 1 A, E Histone H3-like 8355
133 3AZH 1 A, E Histone H3.1 9606
134 5B40 1 A, E Histone H3.2 9606
135 3WAA 1 A, E Histone H3.1 9606
136 5CPI 1 A, E Histone H3.1 9606
137 4JJN 1 A, E Histone H3 4932
138 3W99 1 A, E Histone H3.1 9606
139 3AZE 1 A, E Histone H3.1 9606
140 3W96 1 A, E Histone H3.1 9606
141 5XM1 1 A, E Histone H3mm7 10090
142 5CPJ 1 A, E Histone H3.1 9606
143 5B24 1 A, E Histone H3.1 9606
144 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
145 2HIO 3 C PROTEIN (HISTONE H3) 9031
146 4QLC 3 A, E Histone H3 7227
147 4LD9 1 A, E Histone H3.2 8355
148 3O62 1 A, E Histone H3.2 8355
149 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
150 5KDM 1 A Histone H3.3 9606
151 3W97 1 A, E Histone H3.1 9606
152 4YM5 1 A, E Histone H3.1 9606
153 4YM6 1 A, E Histone H3.1 9606
154 2FJ7 3 A, E histone H3 8355
155 4ZUX 1 A, E, K, O Histone H3.2 8355
156 3AN2 1 A, E Histone H3-like centromeric protein A 9606
157 3B6F 3 A, E Histone H3.2 8355
158 5OY7 2 A, E, I, M, Q, U, Y, c Histone H3 8355
159 3B6G 3 A, E Histone H3.2 8355
160 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
161 3KXB 1 A, E Histone H3.2 8355
162 5HQ2 1 A Histone H3.2 8355
163 5OXV 5 A, E, K, O Histone H3.2 8355
164 1ZBB 3 A, E, a, e HISTONE H3 8355
165 6FML 9 M, Q Histone H3.2 9606
166 6C0W 1 A, E Histone H3-like centromeric protein A 9606
167 6ETX 5 I, M Histone H3.1 9606
168 6ESF 1 A, E Histone H3.2 8355
169 6ESG 1 A, E Histone H3.2 8355
170 6ESH 1 A, E Histone H3.2 8355
171 6ESI 1 A, E Histone H3.2 8355
172 5O9G 1 A, E Histone H3.2 8355
173 5X0X 1 A, E Histone H3.2 8355
174 5X0Y 1 A, E Histone H3.2 8355
175 5KGF 1 A, E Histone H3.2 8355
176 3C9K 3 C, G Histone H3.2 9031