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 2NQB 5 D, H Histone H2B 7227
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 2PYO 6 D, H Histone H2B 7227
35 1P3L 5 D, H Histone H2B 8355
36 1EQZ 3 B, F PROTEIN (HISTONE H2B) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
37 5B0Y 4 D, H Histone H2B type 1-J 9606
38 2CV5 5 D, H Histone H2B K 9606
39 5CP6 6 D, H Histone H2B 1.1 8355
40 5BT1 3 D Histone H2B.1 4932
41 5XF6 4 D, H Histone H2B 1.1 8355
42 3MGP 4 D, H Histone H2B 1.1 8355
43 3MVD 4 D, H Histone H2B 1.1 8355
44 4J8U 4 D, H Histone H2B 1.1 8355
45 4WU9 4 D, H Histone H2B 1.1 8355
46 3REH 4 D, H Histone H2B 1.1 8355
47 3AZL 4 D, H Histone H2B type 1-J 9606
48 3AFA 4 D, H Histone H2B type 1-J 9606
49 5E5A 5 D, H Histone H2B 1.1 8355
50 3REJ 4 D, H Histone H2B 1.1 8355
51 3AZF 4 D, H Histone H2B type 1-J 9606
52 5GTC 4 D, H Histone H2B type 1-J 9606
53 1P3P 5 D, H Histone H2B 8355
54 3AV1 4 D, H Histone H2B type 1-J 9606
55 1M1A 5 D, H Histone H2B.1 8355
56 5CPK 4 D, H Histone H2B type 1-J 9606
57 5AY8 4 D, H Histone H2B type 1-J 9606
58 3MNN 4 D, H Histone H2B 1.1 8355
59 1P3G 5 D, H Histone H2B 8355
60 4J8W 4 D, H Histone H2B 1.1 8355
61 1P34 5 D, H Histone H2B 8355
62 5XF3 4 D, H Histone H2B type 1-J 9606
63 3X1V 5 D, H Histone H2B type 1-A 10090
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 4KUD 4 D, H Histone H2B.1 4932
109 3AZK 4 D, H Histone H2B type 1-J 9606
110 4J8X 4 D, H Histone H2B 1.1 8355
111 3LEL 4 D, H, N, R Histone H2B 1.1 8355
112 3KUY 4 D, H Histone H2B 8355
113 4R8P 4 D, H Histone H2B 1.1 8355
114 3AZM 4 D, H Histone H2B type 1-J 9606
115 3X1U 5 D, H Histone H2B type 1-B 9606
116 3MGS 4 D, H Histone H2B 1.1 8355
117 3WA9 4 D, H Histone H2B type 1-J 9606
118 1ID3 5 D, H HISTONE H2B.2 4932
119 3C1C 4 D, H Histone 2, H2bf 8364
120 3AZH 4 D, H Histone H2B type 1-J 9606
121 5B40 4 D, H Histone H2B type 1-J 9606
122 3WAA 4 D, H Histone H2B type 1-J 9606
123 5CPI 4 D, H Histone H2B type 1-J 9606
124 4JJN 4 D, H Histone H2B.2 4932
125 3W99 4 D, H Histone H2B type 1-J 9606
126 3AZE 4 D, H Histone H2B type 1-J 9606
127 3W96 4 D, H Histone H2B type 1-J 9606
128 5CPJ 4 D, H Histone H2B type 1-J 9606
129 5B24 4 D, H Histone H2B type 1-J 9606
130 2HIO 2 B PROTEIN (HISTONE H2B) 9031
131 4QLC 6 D, H Histone H2B 7227
132 4LD9 4 D, H Histone H2B 1.1 8355
133 3O62 4 D, H Histone H2B 1.1 8355
134 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
135 4YM5 4 D, H Histone H2B type 1-J 9606
136 4YM6 4 D, H Histone H2B type 1-J 9606
137 2FJ7 6 D, H Histone H2B 8355
138 3W98 4 D, H Histone H2B type 1-J 9606
139 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
140 3AN2 4 D, H Histone H2B type 1-J 9606
141 3B6F 6 D, H Histone H2B 1.1 8355
142 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
143 3B6G 6 D, H Histone H2B 1.1 8355
144 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
145 3KXB 4 D, H Histone H2B 1.1 8355
146 5HQ2 4 H Histone H2B 1.1 8355
147 5OXV 2 D, H, N, R Histone H2B 1.1 8355
148 1ZBB 6 D, H, d, h Histone H2B.1 8355
149 5O9G 4 D Histone H2B 1.1 8355
150 5O9G 5 H Histone H2B 1.1 8355
151 5X0X 4 D, H Histone H2B 1.1 8355
152 5X0Y 4 D, H Histone H2B 1.1 8355
153 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
154 2RVQ 2 D Histone H2B type 1-J 9606
155 3C9K 2 B, F Histone H2B 7 9031