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 45 275
95 % 53 157 76 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.1
PDBFlex
90 % 53 160 77
70 % 53 161 89
50 % 54 164 125
40 % 54 164 141
30 % 54 164 155
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 % 52 148 56
95 % 57 167 70 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 58 172 72
70 % 58 172 85
50 % 58 172 117
40 % 58 172 138
30 % 58 172 147
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 57 239
95 % 46 147 78 Flexibility: Low
Max RMSD: 6.7, Avg RMSD: 0.5
PDBFlex
90 % 48 155 78
70 % 50 161 87
50 % 55 171 111
40 % 55 171 134
30 % 55 171 143
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 52 257
95 % 45 143 85 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 45 148 85
70 % 48 155 95
50 % 48 155 133
40 % 48 155 148
30 % 48 155 163
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.


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 5F99 1 A, E Histone H3.2 8355
29 5JRG 1 A, E Histone H3.1 9606
30 3UT9 1 A, E Histone H3.2 8355
31 5B32 1 A, E Histone H3.3 9606
32 4WU8 3 A, E Histone H3.2 8355
33 1P3I 2 A, E Histone H3 8355
34 3MGR 1 A, E Histone H3.2 8355
35 1F66 2 A, E HISTONE H3 8355
36 3AZG 1 A, E Histone H3.1 9606
37 4H9S 1 A, B Histone H3.3 9606
38 1M18 2 A, E Histone H3.2 8355
39 5B2J 1 A, E Histone H3.1 9606
40 2PYO 3 A, E Histone H3 7227
41 1P3L 2 A, E Histone H3 8355
42 1EQZ 4 C, G PROTEIN (HISTONE H3) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
43 5B0Y 1 A, E Histone H3.2 9606
44 2CV5 2 A, E Histone H3.1 9606
45 5CP6 3 A, E Histone H3.2 8355
46 5XF6 1 A, E Histone H3.2 8355
47 3MGP 1 A, E Histone H3.2 8355
48 3MVD 1 A, E Histone H3.2 8355
49 4J8U 1 A, E Histone H3.2 8355
50 4WU9 1 A, E Histone H3.2 8355
51 3REH 1 A, E Histone H3.2 8355
52 3AZL 1 A, E Histone H3.1 9606
53 3AFA 1 A, E Histone H3.1 9606
54 5E5A 2 A, E Histone H3.2 8355
55 3REJ 1 A, E Histone H3.2 8355
56 3AZF 1 A, E Histone H3.1 9606
57 5GTC 1 A, E Histone H3.1 9606
58 1P3P 2 A, E Histone H3 8355
59 3AV1 1 A, E Histone H3.2 9606
60 1M1A 2 A, E Histone H3.2 8355
61 5CPK 1 A, E Histone H3.1 9606
62 3MNN 1 A, E Histone H3.2 8355
63 1P3G 2 A, E Histone H3 8355
64 4J8W 1 A, E Histone H3.2 8355
65 1P34 2 A, E Histone H3 8355
66 5XF3 1 A, E Histone H3.1 9606
67 3X1V 2 A, E Histone H3.1 9606
68 5DNM 1 A, E Histone H3.2 8355
69 4HGA 2 B Histone H3.3 9606
70 4UUZ 1 A HISTONE H3 7227
71 3MGQ 1 A, E Histone H3.2 8355
72 3WTP 5 E Histone H3.3 9606
73 3X1T 2 A, E Histone H3.1 9606
74 2NZD 3 A, E Histone H3 8355
75 3A6N 1 A, E Histone H3.1t 9606
76 5DNN 1 A, E Histone H3.2 8355
77 5GT3 1 A, E Histone H3.1 9606
78 5GT0 1 A, E Histone H3.1 9606
79 3LJA 1 A, E Histone H3.2 8355
80 3AZI 1 A, E Histone H3.1 9606
81 3TU4 1 A, E Histone H3.2 8355
82 1P3O 2 A, E Histone H3 8355
83 1KX4 2 A, E histone H3 8355
84 3AZN 1 A, E Histone H3.1 9606
85 1P3M 2 A, E Histone H3 8355
86 4J8V 1 A, E Histone H3.2 8355
87 5B33 1 A, E Histone H3.3 9606
88 3X1S 1 A, E Histone H3.1 9606
89 3LZ0 1 A, E Histone H3.2 8355
90 1P3F 2 A, E Histone H3 8355
91 1P3K 2 A, E Histone H3 8355
92 5B2I 1 A, E Histone H3.1 9606
93 1P3A 2 A, E Histone H3 8355
94 3LZ1 1 A, E Histone H3.2 8355
95 2IO5 2 B Histone H3.1 8355
96 5GXQ 1 A, E Histone H3.6 9606
97 2F8N 2 A, E Histone H3.1 8355
98 4Z5T 1 A, E Histone H3.3C 9606
99 1U35 2 A, E Histone H3.1 10090
100 3AV2 1 A, E Histone H3.3 9606
101 3AYW 1 A, E Histone H3.1 9606
102 5XF5 1 A, E Histone H3.1 9606
103 3AZJ 1 A, E Histone H3.1 9606
104 3REK 1 A, E Histone H3.2 8355
105 4KGC 1 A, E Histone H3.2 8355
106 1ZLA 2 A, E histone H3 8355
107 5GSU 1 A, E Histone H3.1 9606
108 5XF4 1 A, E Histone H3.1 9606
109 3REL 1 A, E Histone H3.2 8355
110 5GSE 1 A, E, K, O Histone H3.1 9606
111 3REI 1 A, E Histone H3.2 8355
112 1P3B 2 A, E Histone H3 8355
113 3WKJ 1 A, E Histone H3.1 9606
114 4KUD 1 A, E Histone H3 4932
115 3AZK 1 A, E Histone H3.1 9606
116 4J8X 1 A, E Histone H3.2 8355
117 3LEL 1 A, E, K, O Histone H3.2 8355
118 3KUY 1 A, E Histone H3.2 8355
119 4R8P 1 A, E Histone H3.2 8355
120 3AZM 1 A, E Histone H3.1 9606
121 3X1U 2 A, E Histone H3.1 9606
122 3MGS 1 A, E Histone H3.2 8355
123 3WA9 1 A, E Histone H3.1 9606
124 1ID3 2 A, E HISTONE H3 4932
125 3C1C 1 A, E Histone H3-like 8355
126 3AZH 1 A, E Histone H3.1 9606
127 5B40 1 A, E Histone H3.2 9606
128 3WAA 1 A, E Histone H3.1 9606
129 5CPI 1 A, E Histone H3.1 9606
130 4JJN 1 A, E Histone H3 4932
131 3W99 1 A, E Histone H3.1 9606
132 3AZE 1 A, E Histone H3.1 9606
133 3W96 1 A, E Histone H3.1 9606
134 5CPJ 1 A, E Histone H3.1 9606
135 5B24 1 A, E Histone H3.1 9606
136 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
137 2HIO 3 C PROTEIN (HISTONE H3) 9031
138 4QLC 3 A, E Histone H3 7227
139 4LD9 1 A, E Histone H3.2 8355
140 3O62 1 A, E Histone H3.2 8355
141 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
142 5KDM 1 A Histone H3.3 9606
143 3W97 1 A, E Histone H3.1 9606
144 4YM5 1 A, E Histone H3.1 9606
145 4YM6 1 A, E Histone H3.1 9606
146 2FJ7 3 A, E histone H3 8355
147 4ZUX 1 A, E, K, O Histone H3.2 8355
148 3B6F 3 A, E Histone H3.2 8355
149 5OY7 2 A, E, I, M, Q, U, Y, c Histone H3 8355
150 3B6G 3 A, E Histone H3.2 8355
151 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
152 3KXB 1 A, E Histone H3.2 8355
153 5HQ2 1 A Histone H3.2 8355
154 5OXV 5 A, E, K, O Histone H3.2 8355
155 1ZBB 3 A, E, a, e HISTONE H3 8355
156 5O9G 1 A, E Histone H3.2 8355
157 5X0X 1 A, E Histone H3.2 8355
158 5X0Y 1 A, E Histone H3.2 8355
159 5KGF 1 A, E Histone H3.2 8355
160 3C9K 3 C, G Histone H3.2 9031