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 45 283
95 % 54 160 77 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 54 163 76
70 % 54 164 92
50 % 55 167 124
40 % 55 167 143
30 % 55 167 155
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 % 53 151 58
95 % 58 170 70 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 59 175 69
70 % 59 175 82
50 % 59 175 115
40 % 59 175 138
30 % 59 175 145
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 57 245
95 % 47 150 81 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.6
PDBFlex
90 % 49 158 78
70 % 51 164 88
50 % 56 174 111
40 % 56 174 134
30 % 56 174 142
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 52 262
95 % 46 146 84 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 46 151 85
70 % 49 158 98
50 % 49 158 135
40 % 49 158 149
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.


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 5ONG 6 D, H Histone H2B 1.1 8355
66 5ONW 6 D, H Histone H2B 1.1 8355
67 5DNM 4 D, H Histone H2B 1.1 8355
68 3MGQ 4 D, H Histone H2B 1.1 8355
69 3WTP 4 D, H Histone H2B type 1-J 9606
70 3X1T 5 D, H Histone H2B type 1-A 10090
71 2NZD 6 D, H Histone H2B 8355
72 3A6N 4 D, H Histone H2B type 1-J 9606
73 5DNN 4 D, H Histone H2B 1.1 8355
74 5GT3 4 D, H Histone H2B type 1-A 9606
75 5GT0 4 D, H Histone H2B type 1-J 9606
76 3LJA 4 D, H Histone H2B 1.1 8355
77 3AZI 4 D, H Histone H2B type 1-J 9606
78 3TU4 4 D, H Histone H2B 1.1 8355
79 1P3O 5 D, H Histone H2B 8355
80 1KX4 5 D, H histone H2B.2 8355
81 3AZN 4 D, H Histone H2B type 1-J 9606
82 1P3M 5 D, H Histone H2B 8355
83 4J8V 4 D, H Histone H2B 1.1 8355
84 5B33 4 D, H Histone H2B type 1-J 9606
85 3X1S 4 D, H Histone H2B type 1-B 9606
86 3LZ0 4 D, H Histone H2B 1.1 8355
87 1P3F 5 D, H Histone H2B 8355
88 1P3K 5 D, H Histone H2B 8355
89 5B2I 4 D, H Histone H2B type 1-J 9606
90 1P3A 5 D, H Histone H2B 8355
91 3LZ1 4 D, H Histone H2B 1.1 8355
92 5GXQ 4 D, H Histone H2B type 1-J 9606
93 2F8N 4 D Histone 3, H2ba 10090
94 2F8N 5 H Histone H2B.1 8355
95 4Z5T 4 D, H Histone H2B type 1-J 9606
96 1U35 5 D, H histone 3, H2ba 10090
97 3AV2 4 D, H Histone H2B type 1-J 9606
98 3AYW 4 D, H Histone H2B type 1-J 9606
99 5XF5 4 D, H Histone H2B type 1-J 9606
100 3AZJ 4 D, H Histone H2B type 1-J 9606
101 3REK 4 D, H Histone H2B 1.1 8355
102 4KGC 4 D, H Histone H2B 1.1 8355
103 1ZLA 5 D, H histone H2B 8355
104 5GSU 4 D, H Histone H2B type 1-A 9606
105 5XF4 4 D, H Histone H2B type 1-J 9606
106 3REL 4 D, H Histone H2B 1.1 8355
107 5GSE 4 D, H, N Histone H2B type 1-J 9606
108 3REI 4 D, H Histone H2B 1.1 8355
109 1P3B 5 D, H Histone H2B 8355
110 3WKJ 4 D, H Histone H2B type 1-A 9606
111 4KUD 4 D, H Histone H2B.1 4932
112 3AZK 4 D, H Histone H2B type 1-J 9606
113 4J8X 4 D, H Histone H2B 1.1 8355
114 3LEL 4 D, H, N, R Histone H2B 1.1 8355
115 3KUY 4 D, H Histone H2B 8355
116 4R8P 4 D, H Histone H2B 1.1 8355
117 3AZM 4 D, H Histone H2B type 1-J 9606
118 3X1U 5 D, H Histone H2B type 1-B 9606
119 3MGS 4 D, H Histone H2B 1.1 8355
120 3WA9 4 D, H Histone H2B type 1-J 9606
121 1ID3 5 D, H HISTONE H2B.2 4932
122 3C1C 4 D, H Histone 2, H2bf 8364
123 3AZH 4 D, H Histone H2B type 1-J 9606
124 5B40 4 D, H Histone H2B type 1-J 9606
125 3WAA 4 D, H Histone H2B type 1-J 9606
126 5CPI 4 D, H Histone H2B type 1-J 9606
127 4JJN 4 D, H Histone H2B.2 4932
128 3W99 4 D, H Histone H2B type 1-J 9606
129 3AZE 4 D, H Histone H2B type 1-J 9606
130 3W96 4 D, H Histone H2B type 1-J 9606
131 5CPJ 4 D, H Histone H2B type 1-J 9606
132 5B24 4 D, H Histone H2B type 1-J 9606
133 2HIO 2 B PROTEIN (HISTONE H2B) 9031
134 4QLC 6 D, H Histone H2B 7227
135 4LD9 4 D, H Histone H2B 1.1 8355
136 3O62 4 D, H Histone H2B 1.1 8355
137 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
138 4YM5 4 D, H Histone H2B type 1-J 9606
139 4YM6 4 D, H Histone H2B type 1-J 9606
140 2FJ7 6 D, H Histone H2B 8355
141 3W98 4 D, H Histone H2B type 1-J 9606
142 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
143 3AN2 4 D, H Histone H2B type 1-J 9606
144 3B6F 6 D, H Histone H2B 1.1 8355
145 5OY7 1 D, H, L, P, T, X, b, f Histone H2B 1.1 8355
146 3B6G 6 D, H Histone H2B 1.1 8355
147 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
148 3KXB 4 D, H Histone H2B 1.1 8355
149 5HQ2 4 H Histone H2B 1.1 8355
150 5OXV 2 D, H, N, R Histone H2B 1.1 8355
151 1ZBB 6 D, H, d, h Histone H2B.1 8355
152 5O9G 4 D Histone H2B 1.1 8355
153 5O9G 5 H Histone H2B 1.1 8355
154 5X0X 4 D, H Histone H2B 1.1 8355
155 5X0Y 4 D, H Histone H2B 1.1 8355
156 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
157 2RVQ 2 D Histone H2B type 1-J 9606
158 3C9K 2 B, F Histone H2B 7 9031