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 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 5GTC 1 A, E Histone H3.1 9606
57 1P3P 2 A, E Histone H3 8355
58 3AV1 1 A, E Histone H3.2 9606
59 1M1A 2 A, E Histone H3.2 8355
60 5CPK 1 A, E Histone H3.1 9606
61 5AY8 1 A, E H3.Y 9606
62 3MNN 1 A, E Histone H3.2 8355
63 1P3G 2 A, E Histone H3 8355
64 4J8W 1 A, E Histone H3.2 8355
65 1P34 2 A, E Histone H3 8355
66 3X1V 2 A, E Histone H3.1 9606
67 5DNM 1 A, E Histone H3.2 8355
68 4HGA 2 B Histone H3.3 9606
69 4UUZ 1 A HISTONE H3 7227
70 3MGQ 1 A, E Histone H3.2 8355
71 3WTP 5 E Histone H3.3 9606
72 3X1T 2 A, E Histone H3.1 9606
73 2NZD 3 A, E Histone H3 8355
74 3A6N 1 A, E Histone H3.1t 9606
75 5DNN 1 A, E Histone H3.2 8355
76 5GT3 1 A, E Histone H3.1 9606
77 5GT0 1 A, E Histone H3.1 9606
78 3LJA 1 A, E Histone H3.2 8355
79 3AZI 1 A, E Histone H3.1 9606
80 3TU4 1 A, E Histone H3.2 8355
81 1P3O 2 A, E Histone H3 8355
82 1KX4 2 A, E histone H3 8355
83 3AZN 1 A, E Histone H3.1 9606
84 1P3M 2 A, E Histone H3 8355
85 4J8V 1 A, E Histone H3.2 8355
86 5B33 1 A, E Histone H3.3 9606
87 3X1S 1 A, E Histone H3.1 9606
88 3LZ0 1 A, E Histone H3.2 8355
89 1P3F 2 A, E Histone H3 8355
90 1P3K 2 A, E Histone H3 8355
91 5B2I 1 A, E Histone H3.1 9606
92 1P3A 2 A, E Histone H3 8355
93 3LZ1 1 A, E Histone H3.2 8355
94 2IO5 2 B Histone H3.1 8355
95 5GXQ 1 A, E Histone H3.6 9606
96 2F8N 2 A, E Histone H3.1 8355
97 4Z5T 1 A, E Histone H3.3C 9606
98 1U35 2 A, E Histone H3.1 10090
99 3AV2 1 A, E Histone H3.3 9606
100 3AYW 1 A, E Histone H3.1 9606
101 3AZJ 1 A, E Histone H3.1 9606
102 3REK 1 A, E Histone H3.2 8355
103 4KGC 1 A, E Histone H3.2 8355
104 1ZLA 2 A, E histone H3 8355
105 5GSU 1 A, E Histone H3.1 9606
106 3REL 1 A, E Histone H3.2 8355
107 5GSE 1 A, E, K, O Histone H3.1 9606
108 3REI 1 A, E Histone H3.2 8355
109 1P3B 2 A, E Histone H3 8355
110 3WKJ 1 A, E Histone H3.1 9606
111 4KUD 1 A, E Histone H3 4932
112 3AZK 1 A, E Histone H3.1 9606
113 4J8X 1 A, E Histone H3.2 8355
114 3LEL 1 A, E, K, O Histone H3.2 8355
115 3KUY 1 A, E Histone H3.2 8355
116 4R8P 1 A, E Histone H3.2 8355
117 3AZM 1 A, E Histone H3.1 9606
118 3X1U 2 A, E Histone H3.1 9606
119 3MGS 1 A, E Histone H3.2 8355
120 3WA9 1 A, E Histone H3.1 9606
121 1ID3 2 A, E HISTONE H3 4932
122 3C1C 1 A, E Histone H3-like 8355
123 3AZH 1 A, E Histone H3.1 9606
124 5B40 1 A, E Histone H3.2 9606
125 3WAA 1 A, E Histone H3.1 9606
126 5CPI 1 A, E Histone H3.1 9606
127 4JJN 1 A, E Histone H3 4932
128 3W99 1 A, E Histone H3.1 9606
129 3AZE 1 A, E Histone H3.1 9606
130 3W96 1 A, E Histone H3.1 9606
131 5CPJ 1 A, E Histone H3.1 9606
132 5B24 1 A, E Histone H3.1 9606
133 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
134 2HIO 3 C PROTEIN (HISTONE H3) 9031
135 4QLC 3 A, E Histone H3 7227
136 4LD9 1 A, E Histone H3.2 8355
137 3O62 1 A, E Histone H3.2 8355
138 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
139 5KDM 1 A Histone H3.3 9606
140 3W97 1 A, E Histone H3.1 9606
141 4YM5 1 A, E Histone H3.1 9606
142 4YM6 1 A, E Histone H3.1 9606
143 2FJ7 3 A, E histone H3 8355
144 4ZUX 1 A, E, K, O Histone H3.2 8355
145 3B6F 3 A, E Histone H3.2 8355
146 3B6G 3 A, E Histone H3.2 8355
147 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
148 3KXB 1 A, E Histone H3.2 8355
149 5HQ2 1 A Histone H3.2 8355
150 1ZBB 3 A, E, a, e HISTONE H3 8355
151 5X0X 1 A, E Histone H3.2 8355
152 5X0Y 1 A, E Histone H3.2 8355
153 5KGF 1 A, E Histone H3.2 8355
154 3C9K 3 C, G Histone H3.2 9031