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 45 281
95 % 54 158 75 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 54 161 76
70 % 54 162 89
50 % 55 165 125
40 % 55 165 143
30 % 55 165 157
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 % 53 149 56
95 % 58 168 71 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 59 173 72
70 % 59 173 84
50 % 59 173 117
40 % 59 173 139
30 % 59 173 147
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 57 240
95 % 47 148 80 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.6
PDBFlex
90 % 49 156 77
70 % 51 162 87
50 % 56 172 110
40 % 56 172 134
30 % 56 172 143
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 52 260
95 % 46 144 84 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 46 149 84
70 % 49 156 97
50 % 49 156 134
40 % 49 156 149
30 % 49 156 162
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 2NQB 5 D, H Histone H2B 7227
23 5OMX 6 D, H Histone H2B 1.1 8355
24 5F99 4 D, H Histone H2B 1.1 8355
25 5JRG 4 D, H Histone H2B type 1-J 9606
26 3UT9 4 D, H Histone H2B 1.1 8355
27 5B32 4 D, H Histone H2B type 1-J 9606
28 4WU8 6 D, H Histone H2B 1.1 8355
29 1P3I 5 D, H Histone H2B 8355
30 3MGR 4 D, H Histone H2B 1.1 8355
31 1F66 5 D, H HISTONE H2B 8355
32 3AZG 4 D, H Histone H2B type 1-J 9606
33 1M18 5 D, H Histone H2B.1 8355
34 5B2J 4 D, H Histone H2B type 1-J 9606
35 2PYO 6 D, H Histone H2B 7227
36 1P3L 5 D, H Histone H2B 8355
37 1EQZ 3 B, F PROTEIN (HISTONE H2B) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
38 5B0Y 4 D, H Histone H2B type 1-J 9606
39 2CV5 5 D, H Histone H2B K 9606
40 5CP6 6 D, H Histone H2B 1.1 8355
41 5BT1 3 D Histone H2B.1 4932
42 5XF6 4 D, H Histone H2B 1.1 8355
43 3MGP 4 D, H Histone H2B 1.1 8355
44 3MVD 4 D, H Histone H2B 1.1 8355
45 4J8U 4 D, H Histone H2B 1.1 8355
46 4WU9 4 D, H Histone H2B 1.1 8355
47 3REH 4 D, H Histone H2B 1.1 8355
48 3AZL 4 D, H Histone H2B type 1-J 9606
49 3AFA 4 D, H Histone H2B type 1-J 9606
50 5E5A 5 D, H Histone H2B 1.1 8355
51 3REJ 4 D, H Histone H2B 1.1 8355
52 3AZF 4 D, H Histone H2B type 1-J 9606
53 5GTC 4 D, H Histone H2B type 1-J 9606
54 1P3P 5 D, H Histone H2B 8355
55 3AV1 4 D, H Histone H2B type 1-J 9606
56 1M1A 5 D, H Histone H2B.1 8355
57 5CPK 4 D, H Histone H2B type 1-J 9606
58 5AY8 4 D, H Histone H2B type 1-J 9606
59 3MNN 4 D, H Histone H2B 1.1 8355
60 1P3G 5 D, H Histone H2B 8355
61 4J8W 4 D, H Histone H2B 1.1 8355
62 1P34 5 D, H Histone H2B 8355
63 5XF3 4 D, H Histone H2B type 1-J 9606
64 3X1V 5 D, H Histone H2B type 1-A 10090
65 5DNM 4 D, H Histone H2B 1.1 8355
66 3MGQ 4 D, H Histone H2B 1.1 8355
67 3WTP 4 D, H Histone H2B type 1-J 9606
68 3X1T 5 D, H Histone H2B type 1-A 10090
69 2NZD 6 D, H Histone H2B 8355
70 3A6N 4 D, H Histone H2B type 1-J 9606
71 5DNN 4 D, H Histone H2B 1.1 8355
72 5GT3 4 D, H Histone H2B type 1-A 9606
73 5GT0 4 D, H Histone H2B type 1-J 9606
74 3LJA 4 D, H Histone H2B 1.1 8355
75 3AZI 4 D, H Histone H2B type 1-J 9606
76 3TU4 4 D, H Histone H2B 1.1 8355
77 1P3O 5 D, H Histone H2B 8355
78 1KX4 5 D, H histone H2B.2 8355
79 3AZN 4 D, H Histone H2B type 1-J 9606
80 1P3M 5 D, H Histone H2B 8355
81 4J8V 4 D, H Histone H2B 1.1 8355
82 5B33 4 D, H Histone H2B type 1-J 9606
83 3X1S 4 D, H Histone H2B type 1-B 9606
84 3LZ0 4 D, H Histone H2B 1.1 8355
85 1P3F 5 D, H Histone H2B 8355
86 1P3K 5 D, H Histone H2B 8355
87 5B2I 4 D, H Histone H2B type 1-J 9606
88 1P3A 5 D, H Histone H2B 8355
89 3LZ1 4 D, H Histone H2B 1.1 8355
90 5GXQ 4 D, H Histone H2B type 1-J 9606
91 2F8N 4 D Histone 3, H2ba 10090
92 2F8N 5 H Histone H2B.1 8355
93 4Z5T 4 D, H Histone H2B type 1-J 9606
94 1U35 5 D, H histone 3, H2ba 10090
95 3AV2 4 D, H Histone H2B type 1-J 9606
96 3AYW 4 D, H Histone H2B type 1-J 9606
97 5XF5 4 D, H Histone H2B type 1-J 9606
98 3AZJ 4 D, H Histone H2B type 1-J 9606
99 3REK 4 D, H Histone H2B 1.1 8355
100 4KGC 4 D, H Histone H2B 1.1 8355
101 1ZLA 5 D, H histone H2B 8355
102 5GSU 4 D, H Histone H2B type 1-A 9606
103 5XF4 4 D, H Histone H2B type 1-J 9606
104 3REL 4 D, H Histone H2B 1.1 8355
105 5GSE 4 D, H, N Histone H2B type 1-J 9606
106 3REI 4 D, H Histone H2B 1.1 8355
107 1P3B 5 D, H Histone H2B 8355
108 3WKJ 4 D, H Histone H2B type 1-A 9606
109 4KUD 4 D, H Histone H2B.1 4932
110 3AZK 4 D, H Histone H2B type 1-J 9606
111 4J8X 4 D, H Histone H2B 1.1 8355
112 3LEL 4 D, H, N, R Histone H2B 1.1 8355
113 3KUY 4 D, H Histone H2B 8355
114 4R8P 4 D, H Histone H2B 1.1 8355
115 3AZM 4 D, H Histone H2B type 1-J 9606
116 3X1U 5 D, H Histone H2B type 1-B 9606
117 3MGS 4 D, H Histone H2B 1.1 8355
118 3WA9 4 D, H Histone H2B type 1-J 9606
119 1ID3 5 D, H HISTONE H2B.2 4932
120 3C1C 4 D, H Histone 2, H2bf 8364
121 3AZH 4 D, H Histone H2B type 1-J 9606
122 5B40 4 D, H Histone H2B type 1-J 9606
123 3WAA 4 D, H Histone H2B type 1-J 9606
124 5CPI 4 D, H Histone H2B type 1-J 9606
125 4JJN 4 D, H Histone H2B.2 4932
126 3W99 4 D, H Histone H2B type 1-J 9606
127 3AZE 4 D, H Histone H2B type 1-J 9606
128 3W96 4 D, H Histone H2B type 1-J 9606
129 5CPJ 4 D, H Histone H2B type 1-J 9606
130 5B24 4 D, H Histone H2B type 1-J 9606
131 2HIO 2 B PROTEIN (HISTONE H2B) 9031
132 4QLC 6 D, H Histone H2B 7227
133 4LD9 4 D, H Histone H2B 1.1 8355
134 3O62 4 D, H Histone H2B 1.1 8355
135 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
136 4YM5 4 D, H Histone H2B type 1-J 9606
137 4YM6 4 D, H Histone H2B type 1-J 9606
138 2FJ7 6 D, H Histone H2B 8355
139 3W98 4 D, H Histone H2B type 1-J 9606
140 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
141 3AN2 4 D, H Histone H2B type 1-J 9606
142 3B6F 6 D, H Histone H2B 1.1 8355
143 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
144 3B6G 6 D, H Histone H2B 1.1 8355
145 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
146 3KXB 4 D, H Histone H2B 1.1 8355
147 5HQ2 4 H Histone H2B 1.1 8355
148 5OXV 2 D, H, N, R Histone H2B 1.1 8355
149 1ZBB 6 D, H, d, h Histone H2B.1 8355
150 5O9G 4 D Histone H2B 1.1 8355
151 5O9G 5 H Histone H2B 1.1 8355
152 5X0X 4 D, H Histone H2B 1.1 8355
153 5X0Y 4 D, H Histone H2B 1.1 8355
154 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
155 2RVQ 2 D Histone H2B type 1-J 9606
156 3C9K 2 B, F Histone H2B 7 9031