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 42 306
95 % 52 150 77 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 52 153 78
70 % 52 154 96
50 % 53 157 132
40 % 53 157 147
30 % 53 157 161
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 % 51 141 76
95 % 56 160 75 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 57 165 75
70 % 57 165 86
50 % 57 165 124
40 % 57 165 140
30 % 57 165 155
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 54 247
95 % 45 140 86 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.5
PDBFlex
90 % 47 148 79
70 % 49 154 90
50 % 54 164 120
40 % 54 164 139
30 % 54 164 152
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 48 267
95 % 44 135 111 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 44 140 107
70 % 47 147 103
50 % 47 147 140
40 % 47 147 157
30 % 47 147 174
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 3MGP 4 D, H Histone H2B 1.1 8355
39 3MVD 4 D, H Histone H2B 1.1 8355
40 4J8U 4 D, H Histone H2B 1.1 8355
41 4WU9 4 D, H Histone H2B 1.1 8355
42 3REH 4 D, H Histone H2B 1.1 8355
43 3AZL 4 D, H Histone H2B type 1-J 9606
44 3AFA 4 D, H Histone H2B type 1-J 9606
45 5E5A 5 D, H Histone H2B 1.1 8355
46 3REJ 4 D, H Histone H2B 1.1 8355
47 3AZF 4 D, H Histone H2B type 1-J 9606
48 5GTC 4 D, H Histone H2B type 1-J 9606
49 1P3P 5 D, H Histone H2B 8355
50 3AV1 4 D, H Histone H2B type 1-J 9606
51 1M1A 5 D, H Histone H2B.1 8355
52 5CPK 4 D, H Histone H2B type 1-J 9606
53 5AY8 4 D, H Histone H2B type 1-J 9606
54 3MNN 4 D, H Histone H2B 1.1 8355
55 1P3G 5 D, H Histone H2B 8355
56 4J8W 4 D, H Histone H2B 1.1 8355
57 1P34 5 D, H Histone H2B 8355
58 5DNM 4 D, H Histone H2B 1.1 8355
59 3MGQ 4 D, H Histone H2B 1.1 8355
60 3WTP 4 D, H Histone H2B type 1-J 9606
61 2NZD 6 D, H Histone H2B 8355
62 3A6N 4 D, H Histone H2B type 1-J 9606
63 5DNN 4 D, H Histone H2B 1.1 8355
64 5GT0 4 D, H Histone H2B type 1-J 9606
65 3LJA 4 D, H Histone H2B 1.1 8355
66 3AZI 4 D, H Histone H2B type 1-J 9606
67 3TU4 4 D, H Histone H2B 1.1 8355
68 1P3O 5 D, H Histone H2B 8355
69 1KX4 5 D, H histone H2B.2 8355
70 3AZN 4 D, H Histone H2B type 1-J 9606
71 1P3M 5 D, H Histone H2B 8355
72 4J8V 4 D, H Histone H2B 1.1 8355
73 5B33 4 D, H Histone H2B type 1-J 9606
74 3X1S 4 D, H Histone H2B type 1-B 9606
75 3LZ0 4 D, H Histone H2B 1.1 8355
76 1P3F 5 D, H Histone H2B 8355
77 1P3K 5 D, H Histone H2B 8355
78 5B2I 4 D, H Histone H2B type 1-J 9606
79 1P3A 5 D, H Histone H2B 8355
80 3LZ1 4 D, H Histone H2B 1.1 8355
81 5GXQ 4 D, H Histone H2B type 1-J 9606
82 2F8N 4 D Histone 3, H2ba 10090
83 2F8N 5 H Histone H2B.1 8355
84 4Z5T 4 D, H Histone H2B type 1-J 9606
85 1U35 5 D, H histone 3, H2ba 10090
86 3AV2 4 D, H Histone H2B type 1-J 9606
87 3AYW 4 D, H Histone H2B type 1-J 9606
88 3AZJ 4 D, H Histone H2B type 1-J 9606
89 3REK 4 D, H Histone H2B 1.1 8355
90 4KGC 4 D, H Histone H2B 1.1 8355
91 1ZLA 5 D, H histone H2B 8355
92 3REL 4 D, H Histone H2B 1.1 8355
93 5GSE 4 D, H, N Histone H2B type 1-J 9606
94 3REI 4 D, H Histone H2B 1.1 8355
95 1P3B 5 D, H Histone H2B 8355
96 3AZK 4 D, H Histone H2B type 1-J 9606
97 4J8X 4 D, H Histone H2B 1.1 8355
98 3LEL 4 D, H, N, R Histone H2B 1.1 8355
99 3KUY 4 D, H Histone H2B 8355
100 4R8P 4 D, H Histone H2B 1.1 8355
101 3AZM 4 D, H Histone H2B type 1-J 9606
102 3X1U 5 D, H Histone H2B type 1-B 9606
103 3MGS 4 D, H Histone H2B 1.1 8355
104 3WA9 4 D, H Histone H2B type 1-J 9606
105 3C1C 4 D, H Histone 2, H2bf 8364
106 3AZH 4 D, H Histone H2B type 1-J 9606
107 5B40 4 D, H Histone H2B type 1-J 9606
108 3WAA 4 D, H Histone H2B type 1-J 9606
109 5CPI 4 D, H Histone H2B type 1-J 9606
110 3W99 4 D, H Histone H2B type 1-J 9606
111 3AZE 4 D, H Histone H2B type 1-J 9606
112 3W96 4 D, H Histone H2B type 1-J 9606
113 5CPJ 4 D, H Histone H2B type 1-J 9606
114 5B24 4 D, H Histone H2B type 1-J 9606
115 2HIO 2 B PROTEIN (HISTONE H2B) 9031
116 4LD9 4 D, H Histone H2B 1.1 8355
117 3O62 4 D, H Histone H2B 1.1 8355
118 4XUJ 4 D, H Histone H2B 1.1 UNP residues 2-126 8355
119 4YM5 4 D, H Histone H2B type 1-J 9606
120 4YM6 4 D, H Histone H2B type 1-J 9606
121 2FJ7 6 D, H Histone H2B 8355
122 3W98 4 D, H Histone H2B type 1-J 9606
123 4ZUX 4 D, H, N, R Histone H2B 1.1 8355
124 3AN2 4 D, H Histone H2B type 1-J 9606
125 3B6F 6 D, H Histone H2B 1.1 8355
126 3B6G 6 D, H Histone H2B 1.1 8355
127 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
128 3KXB 4 D, H Histone H2B 1.1 8355
129 5HQ2 4 H Histone H2B 1.1 8355
130 1ZBB 6 D, H, d, h Histone H2B.1 8355
131 5X0X 4 D, H Histone H2B 1.1 8355
132 5X0Y 4 D, H Histone H2B 1.1 8355
133 5KGF 4 D, H Histone H2B type 1-C/E/F/G/I 9606
134 2RVQ 2 D Histone H2B type 1-J 9606
135 3C9K 2 B, F Histone H2B 7 9031