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 45 273
95 % 53 157 76 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 53 160 77
70 % 53 161 88
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: 1.3
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 77 Flexibility: Low
Max RMSD: 6.7, Avg RMSD: 0.6
PDBFlex
90 % 48 155 78
70 % 50 161 87
50 % 55 171 111
40 % 55 171 133
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 52 256
95 % 45 143 84 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 45 148 82
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 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 5F99 4 D, H Histone H2B 1.1 8355
23 5JRG 4 D, H Histone H2B type 1-J 9606
24 3UT9 4 D, H Histone H2B 1.1 8355
25 5B32 4 D, H Histone H2B type 1-J 9606
26 4WU8 6 D, H Histone H2B 1.1 8355
27 1P3I 5 D, H Histone H2B 8355
28 3MGR 4 D, H Histone H2B 1.1 8355
29 1F66 5 D, H HISTONE H2B 8355
30 3AZG 4 D, H Histone H2B type 1-J 9606
31 1M18 5 D, H Histone H2B.1 8355
32 5B2J 4 D, H Histone H2B type 1-J 9606
33 1P3L 5 D, H Histone H2B 8355
34 1EQZ 3 B, F PROTEIN (HISTONE H2B) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
35 5B0Y 4 D, H Histone H2B type 1-J 9606
36 2CV5 5 D, H Histone H2B K 9606
37 5CP6 6 D, H Histone H2B 1.1 8355
38 5XF6 4 D, H Histone H2B 1.1 8355
39 3MGP 4 D, H Histone H2B 1.1 8355
40 3MVD 4 D, H Histone H2B 1.1 8355
41 4J8U 4 D, H Histone H2B 1.1 8355
42 4WU9 4 D, H Histone H2B 1.1 8355
43 3REH 4 D, H Histone H2B 1.1 8355
44 3AZL 4 D, H Histone H2B type 1-J 9606
45 3AFA 4 D, H Histone H2B type 1-J 9606
46 5E5A 5 D, H Histone H2B 1.1 8355
47 3REJ 4 D, H Histone H2B 1.1 8355
48 3AZF 4 D, H Histone H2B type 1-J 9606
49 5GTC 4 D, H Histone H2B type 1-J 9606
50 1P3P 5 D, H Histone H2B 8355
51 3AV1 4 D, H Histone H2B type 1-J 9606
52 1M1A 5 D, H Histone H2B.1 8355
53 5CPK 4 D, H Histone H2B type 1-J 9606
54 5AY8 4 D, H Histone H2B type 1-J 9606
55 3MNN 4 D, H Histone H2B 1.1 8355
56 1P3G 5 D, H Histone H2B 8355
57 4J8W 4 D, H Histone H2B 1.1 8355
58 1P34 5 D, H Histone H2B 8355
59 5XF3 4 D, H Histone H2B type 1-J 9606
60 5DNM 4 D, H Histone H2B 1.1 8355
61 3MGQ 4 D, H Histone H2B 1.1 8355
62 3WTP 4 D, H Histone H2B type 1-J 9606
63 2NZD 6 D, H Histone H2B 8355
64 3A6N 4 D, H Histone H2B type 1-J 9606
65 5DNN 4 D, H Histone H2B 1.1 8355
66 5GT0 4 D, H Histone H2B type 1-J 9606
67 3LJA 4 D, H Histone H2B 1.1 8355
68 3AZI 4 D, H Histone H2B type 1-J 9606
69 3TU4 4 D, H Histone H2B 1.1 8355
70 1P3O 5 D, H Histone H2B 8355
71 1KX4 5 D, H histone H2B.2 8355
72 3AZN 4 D, H Histone H2B type 1-J 9606
73 1P3M 5 D, H Histone H2B 8355
74 4J8V 4 D, H Histone H2B 1.1 8355
75 5B33 4 D, H Histone H2B type 1-J 9606
76 3X1S 4 D, H Histone H2B type 1-B 9606
77 3LZ0 4 D, H Histone H2B 1.1 8355
78 1P3F 5 D, H Histone H2B 8355
79 1P3K 5 D, H Histone H2B 8355
80 5B2I 4 D, H Histone H2B type 1-J 9606
81 1P3A 5 D, H Histone H2B 8355
82 3LZ1 4 D, H Histone H2B 1.1 8355
83 5GXQ 4 D, H Histone H2B type 1-J 9606
84 2F8N 4 D Histone 3, H2ba 10090
85 2F8N 5 H Histone H2B.1 8355
86 4Z5T 4 D, H Histone H2B type 1-J 9606
87 1U35 5 D, H histone 3, H2ba 10090
88 3AV2 4 D, H Histone H2B type 1-J 9606
89 3AYW 4 D, H Histone H2B type 1-J 9606
90 5XF5 4 D, H Histone H2B type 1-J 9606
91 3AZJ 4 D, H Histone H2B type 1-J 9606
92 3REK 4 D, H Histone H2B 1.1 8355
93 4KGC 4 D, H Histone H2B 1.1 8355
94 1ZLA 5 D, H histone H2B 8355
95 5XF4 4 D, H Histone H2B type 1-J 9606
96 3REL 4 D, H Histone H2B 1.1 8355
97 5GSE 4 D, H, N Histone H2B type 1-J 9606
98 3REI 4 D, H Histone H2B 1.1 8355
99 1P3B 5 D, H Histone H2B 8355
100 3AZK 4 D, H Histone H2B type 1-J 9606
101 4J8X 4 D, H Histone H2B 1.1 8355
102 3LEL 4 D, H, N, R Histone H2B 1.1 8355
103 3KUY 4 D, H Histone H2B 8355
104 4R8P 4 D, H Histone H2B 1.1 8355
105 3AZM 4 D, H Histone H2B type 1-J 9606
106 3X1U 5 D, H Histone H2B type 1-B 9606
107 3MGS 4 D, H Histone H2B 1.1 8355
108 3WA9 4 D, H Histone H2B type 1-J 9606
109 3C1C 4 D, H Histone 2, H2bf 8364
110 3AZH 4 D, H Histone H2B type 1-J 9606
111 5B40 4 D, H Histone H2B type 1-J 9606
112 3WAA 4 D, H Histone H2B type 1-J 9606
113 5CPI 4 D, H Histone H2B type 1-J 9606
114 3W99 4 D, H Histone H2B type 1-J 9606
115 3AZE 4 D, H Histone H2B type 1-J 9606
116 3W96 4 D, H Histone H2B type 1-J 9606
117 5CPJ 4 D, H Histone H2B type 1-J 9606
118 5B24 4 D, H Histone H2B type 1-J 9606
119 2HIO 2 B PROTEIN (HISTONE H2B) 9031
120 4LD9 4 D, H Histone H2B 1.1 8355
121 3O62 4 D, H Histone H2B 1.1 8355
122 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
123 4YM5 4 D, H Histone H2B type 1-J 9606
124 4YM6 4 D, H Histone H2B type 1-J 9606
125 2FJ7 6 D, H Histone H2B 8355
126 3W98 4 D, H Histone H2B type 1-J 9606
127 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
128 3AN2 4 D, H Histone H2B type 1-J 9606
129 3B6F 6 D, H Histone H2B 1.1 8355
130 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
131 3B6G 6 D, H Histone H2B 1.1 8355
132 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
133 3KXB 4 D, H Histone H2B 1.1 8355
134 5HQ2 4 H Histone H2B 1.1 8355
135 5OXV 2 D, H, N, R Histone H2B 1.1 8355
136 1ZBB 6 D, H, d, h Histone H2B.1 8355
137 5O9G 4 D Histone H2B 1.1 8355
138 5O9G 5 H Histone H2B 1.1 8355
139 5X0X 4 D, H Histone H2B 1.1 8355
140 5X0Y 4 D, H Histone H2B 1.1 8355
141 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
142 2RVQ 2 D Histone H2B type 1-J 9606
143 3C9K 2 B, F Histone H2B 7 9031