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 3NQU 1 A Histone H3-like centromeric protein A 9606
53 3AFA 1 A, E Histone H3.1 9606
54 5E5A 2 A, E Histone H3.2 8355
55 3REJ 1 A, E Histone H3.2 8355
56 3AZF 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 1 A Histone H3-like centromeric protein A 9606
72 3WTP 5 E Histone H3.3 9606
73 3X1T 2 A, E Histone H3.1 9606
74 2NZD 3 A, E Histone H3 8355
75 3A6N 1 A, E Histone H3.1t 9606
76 5DNN 1 A, E Histone H3.2 8355
77 5GT3 1 A, E Histone H3.1 9606
78 5GT0 1 A, E Histone H3.1 9606
79 3LJA 1 A, E Histone H3.2 8355
80 3AZI 1 A, E Histone H3.1 9606
81 3TU4 1 A, E Histone H3.2 8355
82 1P3O 2 A, E Histone H3 8355
83 1KX4 2 A, E histone H3 8355
84 3AZN 1 A, E Histone H3.1 9606
85 1P3M 2 A, E Histone H3 8355
86 4J8V 1 A, E Histone H3.2 8355
87 5B33 1 A, E Histone H3.3 9606
88 3X1S 1 A, E Histone H3.1 9606
89 3LZ0 1 A, E Histone H3.2 8355
90 1P3F 2 A, E Histone H3 8355
91 1P3K 2 A, E Histone H3 8355
92 5B2I 1 A, E Histone H3.1 9606
93 1P3A 2 A, E Histone H3 8355
94 3LZ1 1 A, E Histone H3.2 8355
95 2IO5 2 B Histone H3.1 8355
96 5GXQ 1 A, E Histone H3.6 9606
97 2F8N 2 A, E Histone H3.1 8355
98 4Z5T 1 A, E Histone H3.3C 9606
99 1U35 2 A, E Histone H3.1 10090
100 3AV2 1 A, E Histone H3.3 9606
101 3AYW 1 A, E Histone H3.1 9606
102 3AZJ 1 A, E Histone H3.1 9606
103 3REK 1 A, E Histone H3.2 8355
104 4KGC 1 A, E Histone H3.2 8355
105 1ZLA 2 A, E histone H3 8355
106 5GSU 1 A, E Histone H3.1 9606
107 3REL 1 A, E Histone H3.2 8355
108 5GSE 1 A, E, K, O Histone H3.1 9606
109 3REI 1 A, E Histone H3.2 8355
110 1P3B 2 A, E Histone H3 8355
111 3WKJ 1 A, E Histone H3.1 9606
112 4KUD 1 A, E Histone H3 4932
113 3AZK 1 A, E Histone H3.1 9606
114 4J8X 1 A, E Histone H3.2 8355
115 3LEL 1 A, E, K, O Histone H3.2 8355
116 3KUY 1 A, E Histone H3.2 8355
117 4R8P 1 A, E Histone H3.2 8355
118 3AZM 1 A, E Histone H3.1 9606
119 3X1U 2 A, E Histone H3.1 9606
120 3MGS 1 A, E Histone H3.2 8355
121 3WA9 1 A, E Histone H3.1 9606
122 1ID3 2 A, E HISTONE H3 4932
123 3C1C 1 A, E Histone H3-like 8355
124 3AZH 1 A, E Histone H3.1 9606
125 5B40 1 A, E Histone H3.2 9606
126 3WAA 1 A, E Histone H3.1 9606
127 5CPI 1 A, E Histone H3.1 9606
128 4JJN 1 A, E Histone H3 4932
129 3W99 1 A, E Histone H3.1 9606
130 3AZE 1 A, E Histone H3.1 9606
131 3W96 1 A, E Histone H3.1 9606
132 5CPJ 1 A, E Histone H3.1 9606
133 5B24 1 A, E Histone H3.1 9606
134 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
135 2HIO 3 C PROTEIN (HISTONE H3) 9031
136 4QLC 3 A, E Histone H3 7227
137 4LD9 1 A, E Histone H3.2 8355
138 3O62 1 A, E Histone H3.2 8355
139 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
140 5KDM 1 A Histone H3.3 9606
141 3W97 1 A, E Histone H3.1 9606
142 4YM5 1 A, E Histone H3.1 9606
143 4YM6 1 A, E Histone H3.1 9606
144 2FJ7 3 A, E histone H3 8355
145 4ZUX 1 A, E, K, O Histone H3.2 8355
146 3AN2 1 A, E Histone H3-like centromeric protein A 9606
147 3B6F 3 A, E Histone H3.2 8355
148 3B6G 3 A, E Histone H3.2 8355
149 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
150 3KXB 1 A, E Histone H3.2 8355
151 5HQ2 1 A Histone H3.2 8355
152 1ZBB 3 A, E, a, e HISTONE H3 8355
153 5X0X 1 A, E Histone H3.2 8355
154 5X0Y 1 A, E Histone H3.2 8355
155 5KGF 1 A, E Histone H3.2 8355
156 3C9K 3 C, G Histone H3.2 9031