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 41 305
95 % 52 149 76 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.3
PDBFlex
90 % 52 152 78
70 % 52 153 96
50 % 53 156 132
40 % 53 156 146
30 % 53 156 162
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 % 51 140 75
95 % 56 159 73 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 57 164 75
70 % 57 164 87
50 % 57 164 122
40 % 57 164 140
30 % 57 164 156
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 53 248
95 % 45 139 86 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.5
PDBFlex
90 % 47 147 80
70 % 49 153 88
50 % 54 163 119
40 % 54 163 138
30 % 54 163 152
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 47 266
95 % 44 134 111 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 44 139 108
70 % 47 146 104
50 % 47 146 140
40 % 47 146 155
30 % 47 146 173
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 3 C, G HISTONE H3 9031
2 4H9N 1 A Histone H3.3 9606
3 4H9Q 1 A Histone H3.3 9606
4 1KX5 3 A, E histone H3 8355
5 4H9O 1 A Histone H3.3 9606
6 2ARO 3 C, G HISTONE H3 9031
7 5B0Z 1 A, E Histone H3.2 9606
8 4H9R 1 A Histone H3.3 9606
9 1S32 2 A, E histone H3 8355
10 4H9P 1 A Histone H3.3 9606
11 5AV8 1 A, E Histone H3.1 9606
12 1KX3 2 A, E histone H3 8355
13 5AV9 1 A, E Histone H3.1 9606
14 5AV6 1 A, E Histone H3.1 9606
15 1HQ3 3 C, G HISTONE H3 9031
16 3UTA 1 A, E Histone H3.2 8355
17 5X7X 1 A, E Histone H3.3 9606
18 5B31 1 A, E Histone H3.1 9606
19 5B1L 1 A, E Histone H3t 10090
20 3UTB 1 A, E Histone H3.2 8355
21 1M19 2 A, E Histone H3.2 8355
22 5AVB 1 A, E Histone H3.1 9606
23 5AVC 1 A, E Histone H3.1 9606
24 5AV5 1 A, E Histone H3.1 9606
25 3C1B 1 A, E Histone H3-like 8355
26 5B1M 1 A, E Histone H3.1 10090
27 2NQB 2 A, E Histone H3 7227
28 5F99 1 A, E Histone H3.2 8355
29 5JRG 1 A, E Histone H3.1 9606
30 3UT9 1 A, E Histone H3.2 8355
31 5B32 1 A, E Histone H3.3 9606
32 4WU8 3 A, E Histone H3.2 8355
33 1P3I 2 A, E Histone H3 8355
34 3MGR 1 A, E Histone H3.2 8355
35 1F66 2 A, E HISTONE H3 8355
36 3AZG 1 A, E Histone H3.1 9606
37 4H9S 1 A, B Histone H3.3 9606
38 1M18 2 A, E Histone H3.2 8355
39 5B2J 1 A, E Histone H3.1 9606
40 2PYO 3 A, E Histone H3 7227
41 1P3L 2 A, E Histone H3 8355
42 1EQZ 4 C, G PROTEIN (HISTONE H3) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
43 5B0Y 1 A, E Histone H3.2 9606
44 2CV5 2 A, E Histone H3.1 9606
45 5CP6 3 A, E Histone H3.2 8355
46 3MGP 1 A, E Histone H3.2 8355
47 3MVD 1 A, E Histone H3.2 8355
48 4J8U 1 A, E Histone H3.2 8355
49 4WU9 1 A, E Histone H3.2 8355
50 3REH 1 A, E Histone H3.2 8355
51 3AZL 1 A, E Histone H3.1 9606
52 3AFA 1 A, E Histone H3.1 9606
53 5E5A 2 A, E Histone H3.2 8355
54 3REJ 1 A, E Histone H3.2 8355
55 3AZF 1 A, E Histone H3.1 9606
56 1P3P 2 A, E Histone H3 8355
57 3AV1 1 A, E Histone H3.2 9606
58 1M1A 2 A, E Histone H3.2 8355
59 5CPK 1 A, E Histone H3.1 9606
60 3MNN 1 A, E Histone H3.2 8355
61 1P3G 2 A, E Histone H3 8355
62 4J8W 1 A, E Histone H3.2 8355
63 1P34 2 A, E Histone H3 8355
64 3X1V 2 A, E Histone H3.1 9606
65 5DNM 1 A, E Histone H3.2 8355
66 4HGA 2 B Histone H3.3 9606
67 4UUZ 1 A HISTONE H3 7227
68 3MGQ 1 A, E Histone H3.2 8355
69 3WTP 5 E Histone H3.3 9606
70 3X1T 2 A, E Histone H3.1 9606
71 2NZD 3 A, E Histone H3 8355
72 3A6N 1 A, E Histone H3.1t 9606
73 5DNN 1 A, E Histone H3.2 8355
74 5GT3 1 A, E Histone H3.1 9606
75 5GT0 1 A, E Histone H3.1 9606
76 3LJA 1 A, E Histone H3.2 8355
77 3AZI 1 A, E Histone H3.1 9606
78 3TU4 1 A, E Histone H3.2 8355
79 1P3O 2 A, E Histone H3 8355
80 1KX4 2 A, E histone H3 8355
81 3AZN 1 A, E Histone H3.1 9606
82 1P3M 2 A, E Histone H3 8355
83 4J8V 1 A, E Histone H3.2 8355
84 5B33 1 A, E Histone H3.3 9606
85 3X1S 1 A, E Histone H3.1 9606
86 3LZ0 1 A, E Histone H3.2 8355
87 1P3F 2 A, E Histone H3 8355
88 1P3K 2 A, E Histone H3 8355
89 5B2I 1 A, E Histone H3.1 9606
90 1P3A 2 A, E Histone H3 8355
91 3LZ1 1 A, E Histone H3.2 8355
92 2IO5 2 B Histone H3.1 8355
93 5GXQ 1 A, E Histone H3.6 9606
94 2F8N 2 A, E Histone H3.1 8355
95 4Z5T 1 A, E Histone H3.3C 9606
96 1U35 2 A, E Histone H3.1 10090
97 3AV2 1 A, E Histone H3.3 9606
98 3AYW 1 A, E Histone H3.1 9606
99 3AZJ 1 A, E Histone H3.1 9606
100 3REK 1 A, E Histone H3.2 8355
101 4KGC 1 A, E Histone H3.2 8355
102 1ZLA 2 A, E histone H3 8355
103 5GSU 1 A, E Histone H3.1 9606
104 3REL 1 A, E Histone H3.2 8355
105 5GSE 1 A, E, K, O Histone H3.1 9606
106 3REI 1 A, E Histone H3.2 8355
107 1P3B 2 A, E Histone H3 8355
108 3WKJ 1 A, E Histone H3.1 9606
109 4KUD 1 A, E Histone H3 4932
110 3AZK 1 A, E Histone H3.1 9606
111 4J8X 1 A, E Histone H3.2 8355
112 3LEL 1 A, E, K, O Histone H3.2 8355
113 3KUY 1 A, E Histone H3.2 8355
114 4R8P 1 A, E Histone H3.2 8355
115 3AZM 1 A, E Histone H3.1 9606
116 3X1U 2 A, E Histone H3.1 9606
117 3MGS 1 A, E Histone H3.2 8355
118 3WA9 1 A, E Histone H3.1 9606
119 1ID3 2 A, E HISTONE H3 4932
120 3C1C 1 A, E Histone H3-like 8355
121 3AZH 1 A, E Histone H3.1 9606
122 5B40 1 A, E Histone H3.2 9606
123 3WAA 1 A, E Histone H3.1 9606
124 5CPI 1 A, E Histone H3.1 9606
125 4JJN 1 A, E Histone H3 4932
126 3W99 1 A, E Histone H3.1 9606
127 3AZE 1 A, E Histone H3.1 9606
128 3W96 1 A, E Histone H3.1 9606
129 5CPJ 1 A, E Histone H3.1 9606
130 5B24 1 A, E Histone H3.1 9606
131 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
132 2HIO 3 C PROTEIN (HISTONE H3) 9031
133 4QLC 3 A, E Histone H3 7227
134 4LD9 1 A, E Histone H3.2 8355
135 3O62 1 A, E Histone H3.2 8355
136 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
137 5KDM 1 A Histone H3.3 9606
138 3W97 1 A, E Histone H3.1 9606
139 4YM5 1 A, E Histone H3.1 9606
140 4YM6 1 A, E Histone H3.1 9606
141 2FJ7 3 A, E histone H3 8355
142 4ZUX 1 A, E, K, O Histone H3.2 8355
143 3B6F 3 A, E Histone H3.2 8355
144 3B6G 3 A, E Histone H3.2 8355
145 5NL0 1 A, E, K Histone H3.2 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 1 A, E Histone H3.2 8355
147 5HQ2 1 A Histone H3.2 8355
148 1ZBB 3 A, E, a, e HISTONE H3 8355
149 5X0X 1 A, E Histone H3.2 8355
150 5X0Y 1 A, E Histone H3.2 8355
151 5KGF 1 A, E Histone H3.2 8355
152 3C9K 3 C, G Histone H3.2 9031