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 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 5XF6 1 A, E Histone H3.2 8355
47 3MGP 1 A, E Histone H3.2 8355
48 3MVD 1 A, E Histone H3.2 8355
49 4J8U 1 A, E Histone H3.2 8355
50 4WU9 1 A, E Histone H3.2 8355
51 3REH 1 A, E Histone H3.2 8355
52 3AZL 1 A, E Histone H3.1 9606
53 3NQU 1 A Histone H3-like centromeric protein A 9606
54 3AFA 1 A, E Histone H3.1 9606
55 5E5A 2 A, E Histone H3.2 8355
56 3REJ 1 A, E Histone H3.2 8355
57 3AZF 1 A, E Histone H3.1 9606
58 5GTC 1 A, E Histone H3.1 9606
59 1P3P 2 A, E Histone H3 8355
60 3AV1 1 A, E Histone H3.2 9606
61 1M1A 2 A, E Histone H3.2 8355
62 5CPK 1 A, E Histone H3.1 9606
63 5AY8 1 A, E H3.Y 9606
64 3MNN 1 A, E Histone H3.2 8355
65 1P3G 2 A, E Histone H3 8355
66 4J8W 1 A, E Histone H3.2 8355
67 1P34 2 A, E Histone H3 8355
68 5XF3 1 A, E Histone H3.1 9606
69 3X1V 2 A, E Histone H3.1 9606
70 5DNM 1 A, E Histone H3.2 8355
71 4HGA 2 B Histone H3.3 9606
72 4UUZ 1 A HISTONE H3 7227
73 3MGQ 1 A, E Histone H3.2 8355
74 3WTP 1 A Histone H3-like centromeric protein A 9606
75 3WTP 5 E Histone H3.3 9606
76 3X1T 2 A, E Histone H3.1 9606
77 2NZD 3 A, E Histone H3 8355
78 3A6N 1 A, E Histone H3.1t 9606
79 5DNN 1 A, E Histone H3.2 8355
80 5GT3 1 A, E Histone H3.1 9606
81 5GT0 1 A, E Histone H3.1 9606
82 3LJA 1 A, E Histone H3.2 8355
83 3AZI 1 A, E Histone H3.1 9606
84 3TU4 1 A, E Histone H3.2 8355
85 1P3O 2 A, E Histone H3 8355
86 1KX4 2 A, E histone H3 8355
87 3AZN 1 A, E Histone H3.1 9606
88 1P3M 2 A, E Histone H3 8355
89 4J8V 1 A, E Histone H3.2 8355
90 5B33 1 A, E Histone H3.3 9606
91 3X1S 1 A, E Histone H3.1 9606
92 3LZ0 1 A, E Histone H3.2 8355
93 1P3F 2 A, E Histone H3 8355
94 1P3K 2 A, E Histone H3 8355
95 5B2I 1 A, E Histone H3.1 9606
96 1P3A 2 A, E Histone H3 8355
97 3LZ1 1 A, E Histone H3.2 8355
98 2IO5 2 B Histone H3.1 8355
99 5GXQ 1 A, E Histone H3.6 9606
100 2F8N 2 A, E Histone H3.1 8355
101 4Z5T 1 A, E Histone H3.3C 9606
102 1U35 2 A, E Histone H3.1 10090
103 3AV2 1 A, E Histone H3.3 9606
104 3AYW 1 A, E Histone H3.1 9606
105 5XF5 1 A, E Histone H3.1 9606
106 3AZJ 1 A, E Histone H3.1 9606
107 3REK 1 A, E Histone H3.2 8355
108 4KGC 1 A, E Histone H3.2 8355
109 1ZLA 2 A, E histone H3 8355
110 5GSU 1 A, E Histone H3.1 9606
111 5XF4 1 A, E Histone H3.1 9606
112 3REL 1 A, E Histone H3.2 8355
113 5GSE 1 A, E, K, O Histone H3.1 9606
114 3REI 1 A, E Histone H3.2 8355
115 1P3B 2 A, E Histone H3 8355
116 3WKJ 1 A, E Histone H3.1 9606
117 4KUD 1 A, E Histone H3 4932
118 3AZK 1 A, E Histone H3.1 9606
119 4J8X 1 A, E Histone H3.2 8355
120 3LEL 1 A, E, K, O Histone H3.2 8355
121 3KUY 1 A, E Histone H3.2 8355
122 4R8P 1 A, E Histone H3.2 8355
123 3AZM 1 A, E Histone H3.1 9606
124 3X1U 2 A, E Histone H3.1 9606
125 3MGS 1 A, E Histone H3.2 8355
126 3WA9 1 A, E Histone H3.1 9606
127 1ID3 2 A, E HISTONE H3 4932
128 3C1C 1 A, E Histone H3-like 8355
129 3AZH 1 A, E Histone H3.1 9606
130 5B40 1 A, E Histone H3.2 9606
131 3WAA 1 A, E Histone H3.1 9606
132 5CPI 1 A, E Histone H3.1 9606
133 4JJN 1 A, E Histone H3 4932
134 3W99 1 A, E Histone H3.1 9606
135 3AZE 1 A, E Histone H3.1 9606
136 3W96 1 A, E Histone H3.1 9606
137 5CPJ 1 A, E Histone H3.1 9606
138 5B24 1 A, E Histone H3.1 9606
139 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
140 2HIO 3 C PROTEIN (HISTONE H3) 9031
141 4QLC 3 A, E Histone H3 7227
142 4LD9 1 A, E Histone H3.2 8355
143 3O62 1 A, E Histone H3.2 8355
144 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
145 5KDM 1 A Histone H3.3 9606
146 3W97 1 A, E Histone H3.1 9606
147 4YM5 1 A, E Histone H3.1 9606
148 4YM6 1 A, E Histone H3.1 9606
149 2FJ7 3 A, E histone H3 8355
150 4ZUX 1 A, E, K, O Histone H3.2 8355
151 3AN2 1 A, E Histone H3-like centromeric protein A 9606
152 3B6F 3 A, E Histone H3.2 8355
153 5OY7 2 A, E, I, M, Q, U, Y, c Histone H3 8355
154 3B6G 3 A, E Histone H3.2 8355
155 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
156 3KXB 1 A, E Histone H3.2 8355
157 5HQ2 1 A Histone H3.2 8355
158 5OXV 5 A, E, K, O Histone H3.2 8355
159 1ZBB 3 A, E, a, e HISTONE H3 8355
160 5O9G 1 A, E Histone H3.2 8355
161 5X0X 1 A, E Histone H3.2 8355
162 5X0Y 1 A, E Histone H3.2 8355
163 5KGF 1 A, E Histone H3.2 8355
164 3C9K 3 C, G Histone H3.2 9031