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 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 3X1V 5 D, H Histone H2B type 1-A 10090
61 5DNM 4 D, H Histone H2B 1.1 8355
62 3MGQ 4 D, H Histone H2B 1.1 8355
63 3WTP 4 D, H Histone H2B type 1-J 9606
64 3X1T 5 D, H Histone H2B type 1-A 10090
65 2NZD 6 D, H Histone H2B 8355
66 3A6N 4 D, H Histone H2B type 1-J 9606
67 5DNN 4 D, H Histone H2B 1.1 8355
68 5GT3 4 D, H Histone H2B type 1-A 9606
69 5GT0 4 D, H Histone H2B type 1-J 9606
70 3LJA 4 D, H Histone H2B 1.1 8355
71 3AZI 4 D, H Histone H2B type 1-J 9606
72 3TU4 4 D, H Histone H2B 1.1 8355
73 1P3O 5 D, H Histone H2B 8355
74 1KX4 5 D, H histone H2B.2 8355
75 3AZN 4 D, H Histone H2B type 1-J 9606
76 1P3M 5 D, H Histone H2B 8355
77 4J8V 4 D, H Histone H2B 1.1 8355
78 5B33 4 D, H Histone H2B type 1-J 9606
79 3X1S 4 D, H Histone H2B type 1-B 9606
80 3LZ0 4 D, H Histone H2B 1.1 8355
81 1P3F 5 D, H Histone H2B 8355
82 1P3K 5 D, H Histone H2B 8355
83 5B2I 4 D, H Histone H2B type 1-J 9606
84 1P3A 5 D, H Histone H2B 8355
85 3LZ1 4 D, H Histone H2B 1.1 8355
86 5GXQ 4 D, H Histone H2B type 1-J 9606
87 2F8N 4 D Histone 3, H2ba 10090
88 2F8N 5 H Histone H2B.1 8355
89 4Z5T 4 D, H Histone H2B type 1-J 9606
90 1U35 5 D, H histone 3, H2ba 10090
91 3AV2 4 D, H Histone H2B type 1-J 9606
92 3AYW 4 D, H Histone H2B type 1-J 9606
93 5XF5 4 D, H Histone H2B type 1-J 9606
94 3AZJ 4 D, H Histone H2B type 1-J 9606
95 3REK 4 D, H Histone H2B 1.1 8355
96 4KGC 4 D, H Histone H2B 1.1 8355
97 1ZLA 5 D, H histone H2B 8355
98 5GSU 4 D, H Histone H2B type 1-A 9606
99 5XF4 4 D, H Histone H2B type 1-J 9606
100 3REL 4 D, H Histone H2B 1.1 8355
101 5GSE 4 D, H, N Histone H2B type 1-J 9606
102 3REI 4 D, H Histone H2B 1.1 8355
103 1P3B 5 D, H Histone H2B 8355
104 3WKJ 4 D, H Histone H2B type 1-A 9606
105 3AZK 4 D, H Histone H2B type 1-J 9606
106 4J8X 4 D, H Histone H2B 1.1 8355
107 3LEL 4 D, H, N, R Histone H2B 1.1 8355
108 3KUY 4 D, H Histone H2B 8355
109 4R8P 4 D, H Histone H2B 1.1 8355
110 3AZM 4 D, H Histone H2B type 1-J 9606
111 3X1U 5 D, H Histone H2B type 1-B 9606
112 3MGS 4 D, H Histone H2B 1.1 8355
113 3WA9 4 D, H Histone H2B type 1-J 9606
114 3C1C 4 D, H Histone 2, H2bf 8364
115 3AZH 4 D, H Histone H2B type 1-J 9606
116 5B40 4 D, H Histone H2B type 1-J 9606
117 3WAA 4 D, H Histone H2B type 1-J 9606
118 5CPI 4 D, H Histone H2B type 1-J 9606
119 3W99 4 D, H Histone H2B type 1-J 9606
120 3AZE 4 D, H Histone H2B type 1-J 9606
121 3W96 4 D, H Histone H2B type 1-J 9606
122 5CPJ 4 D, H Histone H2B type 1-J 9606
123 5B24 4 D, H Histone H2B type 1-J 9606
124 2HIO 2 B PROTEIN (HISTONE H2B) 9031
125 4LD9 4 D, H Histone H2B 1.1 8355
126 3O62 4 D, H Histone H2B 1.1 8355
127 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
128 4YM5 4 D, H Histone H2B type 1-J 9606
129 4YM6 4 D, H Histone H2B type 1-J 9606
130 2FJ7 6 D, H Histone H2B 8355
131 3W98 4 D, H Histone H2B type 1-J 9606
132 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
133 3AN2 4 D, H Histone H2B type 1-J 9606
134 3B6F 6 D, H Histone H2B 1.1 8355
135 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
136 3B6G 6 D, H Histone H2B 1.1 8355
137 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
138 3KXB 4 D, H Histone H2B 1.1 8355
139 5HQ2 4 H Histone H2B 1.1 8355
140 5OXV 2 D, H, N, R Histone H2B 1.1 8355
141 1ZBB 6 D, H, d, h Histone H2B.1 8355
142 5O9G 4 D Histone H2B 1.1 8355
143 5O9G 5 H Histone H2B 1.1 8355
144 5X0X 4 D, H Histone H2B 1.1 8355
145 5X0Y 4 D, H Histone H2B 1.1 8355
146 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
147 2RVQ 2 D Histone H2B type 1-J 9606
148 3C9K 2 B, F Histone H2B 7 9031