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 45 310
95 % 54 160 77 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 54 163 77
70 % 54 164 92
50 % 55 167 125
40 % 55 167 145
30 % 55 167 156
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 % 53 151 58
95 % 58 170 71 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 59 175 69
70 % 59 175 83
50 % 59 175 116
40 % 59 175 139
30 % 59 175 144
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 57 247
95 % 47 150 81 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.6
PDBFlex
90 % 49 158 79
70 % 51 164 89
50 % 56 174 111
40 % 56 174 135
30 % 56 174 141
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 52 263
95 % 46 146 85 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 46 151 85
70 % 49 158 98
50 % 49 158 136
40 % 49 158 151
30 % 49 158 161
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 3AFA 1 A, E Histone H3.1 9606
55 5E5A 2 A, E Histone H3.2 8355
56 3REJ 1 A, E Histone H3.2 8355
57 3AZF 1 A, E Histone H3.1 9606
58 5GTC 1 A, E Histone H3.1 9606
59 1P3P 2 A, E Histone H3 8355
60 3AV1 1 A, E Histone H3.2 9606
61 1M1A 2 A, E Histone H3.2 8355
62 5CPK 1 A, E Histone H3.1 9606
63 5AY8 1 A, E H3.Y 9606
64 3MNN 1 A, E Histone H3.2 8355
65 1P3G 2 A, E Histone H3 8355
66 4J8W 1 A, E Histone H3.2 8355
67 1P34 2 A, E Histone H3 8355
68 5XF3 1 A, E Histone H3.1 9606
69 3X1V 2 A, E Histone H3.1 9606
70 5ONG 3 A, E Histone H3.2 8355
71 5ONW 3 A, E Histone H3.2 8355
72 5DNM 1 A, E Histone H3.2 8355
73 4HGA 2 B Histone H3.3 9606
74 4UUZ 1 A HISTONE H3 7227
75 3MGQ 1 A, E Histone H3.2 8355
76 3WTP 5 E Histone H3.3 9606
77 3X1T 2 A, E Histone H3.1 9606
78 2NZD 3 A, E Histone H3 8355
79 3A6N 1 A, E Histone H3.1t 9606
80 5DNN 1 A, E Histone H3.2 8355
81 5GT3 1 A, E Histone H3.1 9606
82 5GT0 1 A, E Histone H3.1 9606
83 3LJA 1 A, E Histone H3.2 8355
84 3AZI 1 A, E Histone H3.1 9606
85 3TU4 1 A, E Histone H3.2 8355
86 1P3O 2 A, E Histone H3 8355
87 1KX4 2 A, E histone H3 8355
88 3AZN 1 A, E Histone H3.1 9606
89 1P3M 2 A, E Histone H3 8355
90 4J8V 1 A, E Histone H3.2 8355
91 5B33 1 A, E Histone H3.3 9606
92 3X1S 1 A, E Histone H3.1 9606
93 3LZ0 1 A, E Histone H3.2 8355
94 1P3F 2 A, E Histone H3 8355
95 1P3K 2 A, E Histone H3 8355
96 5B2I 1 A, E Histone H3.1 9606
97 1P3A 2 A, E Histone H3 8355
98 3LZ1 1 A, E Histone H3.2 8355
99 2IO5 2 B Histone H3.1 8355
100 5GXQ 1 A, E Histone H3.6 9606
101 2F8N 2 A, E Histone H3.1 8355
102 4Z5T 1 A, E Histone H3.3C 9606
103 1U35 2 A, E Histone H3.1 10090
104 3AV2 1 A, E Histone H3.3 9606
105 3AYW 1 A, E Histone H3.1 9606
106 5XF5 1 A, E Histone H3.1 9606
107 3AZJ 1 A, E Histone H3.1 9606
108 3REK 1 A, E Histone H3.2 8355
109 4KGC 1 A, E Histone H3.2 8355
110 1ZLA 2 A, E histone H3 8355
111 5GSU 1 A, E Histone H3.1 9606
112 5XF4 1 A, E Histone H3.1 9606
113 3REL 1 A, E Histone H3.2 8355
114 5GSE 1 A, E, K, O Histone H3.1 9606
115 3REI 1 A, E Histone H3.2 8355
116 1P3B 2 A, E Histone H3 8355
117 3WKJ 1 A, E Histone H3.1 9606
118 4KUD 1 A, E Histone H3 4932
119 3AZK 1 A, E Histone H3.1 9606
120 4J8X 1 A, E Histone H3.2 8355
121 3LEL 1 A, E, K, O Histone H3.2 8355
122 3KUY 1 A, E Histone H3.2 8355
123 4R8P 1 A, E Histone H3.2 8355
124 3AZM 1 A, E Histone H3.1 9606
125 3X1U 2 A, E Histone H3.1 9606
126 3MGS 1 A, E Histone H3.2 8355
127 3WA9 1 A, E Histone H3.1 9606
128 1ID3 2 A, E HISTONE H3 4932
129 3C1C 1 A, E Histone H3-like 8355
130 3AZH 1 A, E Histone H3.1 9606
131 5B40 1 A, E Histone H3.2 9606
132 3WAA 1 A, E Histone H3.1 9606
133 5CPI 1 A, E Histone H3.1 9606
134 4JJN 1 A, E Histone H3 4932
135 3W99 1 A, E Histone H3.1 9606
136 3AZE 1 A, E Histone H3.1 9606
137 3W96 1 A, E Histone H3.1 9606
138 5CPJ 1 A, E Histone H3.1 9606
139 5B24 1 A, E Histone H3.1 9606
140 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
141 2HIO 3 C PROTEIN (HISTONE H3) 9031
142 4QLC 3 A, E Histone H3 7227
143 4LD9 1 A, E Histone H3.2 8355
144 3O62 1 A, E Histone H3.2 8355
145 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
146 5KDM 1 A Histone H3.3 9606
147 3W97 1 A, E Histone H3.1 9606
148 4YM5 1 A, E Histone H3.1 9606
149 4YM6 1 A, E Histone H3.1 9606
150 2FJ7 3 A, E histone H3 8355
151 4ZUX 1 A, E, K, O Histone H3.2 8355
152 3B6F 3 A, E Histone H3.2 8355
153 5OY7 2 A, E, I, M, Q, U, Y, c Histone H3 8355
154 3B6G 3 A, E Histone H3.2 8355
155 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
156 3KXB 1 A, E Histone H3.2 8355
157 5HQ2 1 A Histone H3.2 8355
158 5OXV 5 A, E, K, O Histone H3.2 8355
159 1ZBB 3 A, E, a, e HISTONE H3 8355
160 5O9G 1 A, E Histone H3.2 8355
161 5X0X 1 A, E Histone H3.2 8355
162 5X0Y 1 A, E Histone H3.2 8355
163 5KGF 1 A, E Histone H3.2 8355
164 3C9K 3 C, G Histone H3.2 9031