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 2 B, F Histone H2B 9031
2 1KX5 6 D, H histone H2B.2 8355
3 2ARO 2 B, F Histone H2B 9031
4 5B0Z 4 D, H Histone H2B type 1-J 9606
5 1S32 5 D, H Histone H2B 8355
6 5AV8 4 D, H Histone H2B type 1-J 9606
7 1KX3 5 D, H histone H2B.2 8355
8 5AV9 4 D, H Histone H2B type 1-J 9606
9 5AV6 4 D, H Histone H2B type 1-J 9606
10 1HQ3 2 B, F HISTONE H2B 9031
11 3UTA 4 D, H Histone H2B 1.1 8355
12 5X7X 4 D, H Histone H2B type 1-J 9606
13 5B31 4 D, H Histone H2B type 1-J 9606
14 5B1L 4 D, H Histone H2B type 3-A 10090
15 3UTB 4 D, H Histone H2B 1.1 8355
16 1M19 5 D, H Histone H2B.1 8355
17 5AVB 4 D, H Histone H2B type 1-J 9606
18 5AVC 4 D, H Histone H2B type 1-J 9606
19 5AV5 4 D, H Histone H2B type 1-J 9606
20 3C1B 4 D, H Histone 2, H2bf 8364
21 5B1M 4 D, H Histone H2B type 3-A 10090
22 5OMX 6 D, H Histone H2B 1.1 8355
23 5F99 4 D, H Histone H2B 1.1 8355
24 5JRG 4 D, H Histone H2B type 1-J 9606
25 3UT9 4 D, H Histone H2B 1.1 8355
26 5B32 4 D, H Histone H2B type 1-J 9606
27 4WU8 6 D, H Histone H2B 1.1 8355
28 1P3I 5 D, H Histone H2B 8355
29 3MGR 4 D, H Histone H2B 1.1 8355
30 1F66 5 D, H HISTONE H2B 8355
31 3AZG 4 D, H Histone H2B type 1-J 9606
32 1M18 5 D, H Histone H2B.1 8355
33 5B2J 4 D, H Histone H2B type 1-J 9606
34 1P3L 5 D, H Histone H2B 8355
35 1EQZ 3 B, F PROTEIN (HISTONE H2B) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
36 5B0Y 4 D, H Histone H2B type 1-J 9606
37 2CV5 5 D, H Histone H2B K 9606
38 5CP6 6 D, H Histone H2B 1.1 8355
39 5XF6 4 D, H Histone H2B 1.1 8355
40 3MGP 4 D, H Histone H2B 1.1 8355
41 3MVD 4 D, H Histone H2B 1.1 8355
42 4J8U 4 D, H Histone H2B 1.1 8355
43 4WU9 4 D, H Histone H2B 1.1 8355
44 3REH 4 D, H Histone H2B 1.1 8355
45 3AZL 4 D, H Histone H2B type 1-J 9606
46 3AFA 4 D, H Histone H2B type 1-J 9606
47 5E5A 5 D, H Histone H2B 1.1 8355
48 3REJ 4 D, H Histone H2B 1.1 8355
49 3AZF 4 D, H Histone H2B type 1-J 9606
50 5GTC 4 D, H Histone H2B type 1-J 9606
51 1P3P 5 D, H Histone H2B 8355
52 3AV1 4 D, H Histone H2B type 1-J 9606
53 1M1A 5 D, H Histone H2B.1 8355
54 5CPK 4 D, H Histone H2B type 1-J 9606
55 5AY8 4 D, H Histone H2B type 1-J 9606
56 3MNN 4 D, H Histone H2B 1.1 8355
57 1P3G 5 D, H Histone H2B 8355
58 4J8W 4 D, H Histone H2B 1.1 8355
59 1P34 5 D, H Histone H2B 8355
60 5XF3 4 D, H Histone H2B type 1-J 9606
61 3X1V 5 D, H Histone H2B type 1-A 10090
62 5ONG 6 D, H Histone H2B 1.1 8355
63 5ONW 6 D, H Histone H2B 1.1 8355
64 5DNM 4 D, H Histone H2B 1.1 8355
65 3MGQ 4 D, H Histone H2B 1.1 8355
66 3WTP 4 D, H Histone H2B type 1-J 9606
67 3X1T 5 D, H Histone H2B type 1-A 10090
68 2NZD 6 D, H Histone H2B 8355
69 3A6N 4 D, H Histone H2B type 1-J 9606
70 5DNN 4 D, H Histone H2B 1.1 8355
71 5GT3 4 D, H Histone H2B type 1-A 9606
72 5GT0 4 D, H Histone H2B type 1-J 9606
73 3LJA 4 D, H Histone H2B 1.1 8355
74 3AZI 4 D, H Histone H2B type 1-J 9606
75 3TU4 4 D, H Histone H2B 1.1 8355
76 1P3O 5 D, H Histone H2B 8355
77 1KX4 5 D, H histone H2B.2 8355
78 3AZN 4 D, H Histone H2B type 1-J 9606
79 1P3M 5 D, H Histone H2B 8355
80 4J8V 4 D, H Histone H2B 1.1 8355
81 5B33 4 D, H Histone H2B type 1-J 9606
82 3X1S 4 D, H Histone H2B type 1-B 9606
83 3LZ0 4 D, H Histone H2B 1.1 8355
84 1P3F 5 D, H Histone H2B 8355
85 1P3K 5 D, H Histone H2B 8355
86 5B2I 4 D, H Histone H2B type 1-J 9606
87 1P3A 5 D, H Histone H2B 8355
88 3LZ1 4 D, H Histone H2B 1.1 8355
89 5GXQ 4 D, H Histone H2B type 1-J 9606
90 2F8N 4 D Histone 3, H2ba 10090
91 2F8N 5 H Histone H2B.1 8355
92 4Z5T 4 D, H Histone H2B type 1-J 9606
93 1U35 5 D, H histone 3, H2ba 10090
94 3AV2 4 D, H Histone H2B type 1-J 9606
95 3AYW 4 D, H Histone H2B type 1-J 9606
96 5XF5 4 D, H Histone H2B type 1-J 9606
97 3AZJ 4 D, H Histone H2B type 1-J 9606
98 3REK 4 D, H Histone H2B 1.1 8355
99 4KGC 4 D, H Histone H2B 1.1 8355
100 1ZLA 5 D, H histone H2B 8355
101 5GSU 4 D, H Histone H2B type 1-A 9606
102 5XF4 4 D, H Histone H2B type 1-J 9606
103 3REL 4 D, H Histone H2B 1.1 8355
104 5GSE 4 D, H, N Histone H2B type 1-J 9606
105 3REI 4 D, H Histone H2B 1.1 8355
106 1P3B 5 D, H Histone H2B 8355
107 3WKJ 4 D, H Histone H2B type 1-A 9606
108 3AZK 4 D, H Histone H2B type 1-J 9606
109 4J8X 4 D, H Histone H2B 1.1 8355
110 3LEL 4 D, H, N, R Histone H2B 1.1 8355
111 3KUY 4 D, H Histone H2B 8355
112 4R8P 4 D, H Histone H2B 1.1 8355
113 3AZM 4 D, H Histone H2B type 1-J 9606
114 3X1U 5 D, H Histone H2B type 1-B 9606
115 3MGS 4 D, H Histone H2B 1.1 8355
116 3WA9 4 D, H Histone H2B type 1-J 9606
117 3C1C 4 D, H Histone 2, H2bf 8364
118 3AZH 4 D, H Histone H2B type 1-J 9606
119 5B40 4 D, H Histone H2B type 1-J 9606
120 3WAA 4 D, H Histone H2B type 1-J 9606
121 5CPI 4 D, H Histone H2B type 1-J 9606
122 3W99 4 D, H Histone H2B type 1-J 9606
123 3AZE 4 D, H Histone H2B type 1-J 9606
124 3W96 4 D, H Histone H2B type 1-J 9606
125 5CPJ 4 D, H Histone H2B type 1-J 9606
126 5B24 4 D, H Histone H2B type 1-J 9606
127 2HIO 2 B PROTEIN (HISTONE H2B) 9031
128 4LD9 4 D, H Histone H2B 1.1 8355
129 3O62 4 D, H Histone H2B 1.1 8355
130 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
131 4YM5 4 D, H Histone H2B type 1-J 9606
132 4YM6 4 D, H Histone H2B type 1-J 9606
133 2FJ7 6 D, H Histone H2B 8355
134 3W98 4 D, H Histone H2B type 1-J 9606
135 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
136 3AN2 4 D, H Histone H2B type 1-J 9606
137 3B6F 6 D, H Histone H2B 1.1 8355
138 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
139 3B6G 6 D, H Histone H2B 1.1 8355
140 5NL0 4 D, H, N Histone H2B 1.1 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
141 3KXB 4 D, H Histone H2B 1.1 8355
142 5HQ2 4 H Histone H2B 1.1 8355
143 5OXV 2 D, H, N, R Histone H2B 1.1 8355
144 1ZBB 6 D, H, d, h Histone H2B.1 8355
145 5O9G 4 D Histone H2B 1.1 8355
146 5O9G 5 H Histone H2B 1.1 8355
147 5X0X 4 D, H Histone H2B 1.1 8355
148 5X0Y 4 D, H Histone H2B 1.1 8355
149 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
150 2RVQ 2 D Histone H2B type 1-J 9606
151 3C9K 2 B, F Histone H2B 7 9031