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 45 283
95 % 54 160 77 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 54 163 76
70 % 54 164 92
50 % 55 167 124
40 % 55 167 143
30 % 55 167 155
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 % 53 151 58
95 % 58 170 70 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 59 175 69
70 % 59 175 82
50 % 59 175 115
40 % 59 175 138
30 % 59 175 145
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 57 245
95 % 47 150 81 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.6
PDBFlex
90 % 49 158 78
70 % 51 164 88
50 % 56 174 111
40 % 56 174 134
30 % 56 174 142
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 52 262
95 % 46 146 84 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 46 151 85
70 % 49 158 98
50 % 49 158 135
40 % 49 158 149
30 % 49 158 161
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 5OMX 3 A, E Histone H3.2 8355
29 5F99 1 A, E Histone H3.2 8355
30 5JRG 1 A, E Histone H3.1 9606
31 3UT9 1 A, E Histone H3.2 8355
32 5B32 1 A, E Histone H3.3 9606
33 4WU8 3 A, E Histone H3.2 8355
34 1P3I 2 A, E Histone H3 8355
35 3MGR 1 A, E Histone H3.2 8355
36 1F66 2 A, E HISTONE H3 8355
37 3AZG 1 A, E Histone H3.1 9606
38 4H9S 1 A, B Histone H3.3 9606
39 1M18 2 A, E Histone H3.2 8355
40 5B2J 1 A, E Histone H3.1 9606
41 2PYO 3 A, E Histone H3 7227
42 1P3L 2 A, E Histone H3 8355
43 1EQZ 4 C, G PROTEIN (HISTONE H3) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
44 5B0Y 1 A, E Histone H3.2 9606
45 2CV5 2 A, E Histone H3.1 9606
46 5CP6 3 A, E Histone H3.2 8355
47 5XF6 1 A, E Histone H3.2 8355
48 3MGP 1 A, E Histone H3.2 8355
49 3MVD 1 A, E Histone H3.2 8355
50 4J8U 1 A, E Histone H3.2 8355
51 4WU9 1 A, E Histone H3.2 8355
52 3REH 1 A, E Histone H3.2 8355
53 3AZL 1 A, E Histone H3.1 9606
54 3NQU 1 A Histone H3-like centromeric protein A 9606
55 3AFA 1 A, E Histone H3.1 9606
56 5E5A 2 A, E Histone H3.2 8355
57 3REJ 1 A, E Histone H3.2 8355
58 3AZF 1 A, E Histone H3.1 9606
59 5GTC 1 A, E Histone H3.1 9606
60 1P3P 2 A, E Histone H3 8355
61 3AV1 1 A, E Histone H3.2 9606
62 1M1A 2 A, E Histone H3.2 8355
63 5CPK 1 A, E Histone H3.1 9606
64 5AY8 1 A, E H3.Y 9606
65 3MNN 1 A, E Histone H3.2 8355
66 1P3G 2 A, E Histone H3 8355
67 4J8W 1 A, E Histone H3.2 8355
68 1P34 2 A, E Histone H3 8355
69 5XF3 1 A, E Histone H3.1 9606
70 3X1V 2 A, E Histone H3.1 9606
71 5ONG 3 A, E Histone H3.2 8355
72 5ONW 3 A, E Histone H3.2 8355
73 5DNM 1 A, E Histone H3.2 8355
74 4HGA 2 B Histone H3.3 9606
75 4UUZ 1 A HISTONE H3 7227
76 3MGQ 1 A, E Histone H3.2 8355
77 3WTP 1 A Histone H3-like centromeric protein A 9606
78 3WTP 5 E Histone H3.3 9606
79 3X1T 2 A, E Histone H3.1 9606
80 2NZD 3 A, E Histone H3 8355
81 3A6N 1 A, E Histone H3.1t 9606
82 5DNN 1 A, E Histone H3.2 8355
83 5GT3 1 A, E Histone H3.1 9606
84 5GT0 1 A, E Histone H3.1 9606
85 3LJA 1 A, E Histone H3.2 8355
86 3AZI 1 A, E Histone H3.1 9606
87 3TU4 1 A, E Histone H3.2 8355
88 1P3O 2 A, E Histone H3 8355
89 1KX4 2 A, E histone H3 8355
90 3AZN 1 A, E Histone H3.1 9606
91 1P3M 2 A, E Histone H3 8355
92 4J8V 1 A, E Histone H3.2 8355
93 5B33 1 A, E Histone H3.3 9606
94 3X1S 1 A, E Histone H3.1 9606
95 3LZ0 1 A, E Histone H3.2 8355
96 1P3F 2 A, E Histone H3 8355
97 1P3K 2 A, E Histone H3 8355
98 5B2I 1 A, E Histone H3.1 9606
99 1P3A 2 A, E Histone H3 8355
100 3LZ1 1 A, E Histone H3.2 8355
101 2IO5 2 B Histone H3.1 8355
102 5GXQ 1 A, E Histone H3.6 9606
103 2F8N 2 A, E Histone H3.1 8355
104 4Z5T 1 A, E Histone H3.3C 9606
105 1U35 2 A, E Histone H3.1 10090
106 3AV2 1 A, E Histone H3.3 9606
107 3AYW 1 A, E Histone H3.1 9606
108 5XF5 1 A, E Histone H3.1 9606
109 3AZJ 1 A, E Histone H3.1 9606
110 3REK 1 A, E Histone H3.2 8355
111 4KGC 1 A, E Histone H3.2 8355
112 1ZLA 2 A, E histone H3 8355
113 5GSU 1 A, E Histone H3.1 9606
114 5XF4 1 A, E Histone H3.1 9606
115 3REL 1 A, E Histone H3.2 8355
116 5GSE 1 A, E, K, O Histone H3.1 9606
117 3REI 1 A, E Histone H3.2 8355
118 1P3B 2 A, E Histone H3 8355
119 3WKJ 1 A, E Histone H3.1 9606
120 4KUD 1 A, E Histone H3 4932
121 3AZK 1 A, E Histone H3.1 9606
122 4J8X 1 A, E Histone H3.2 8355
123 3LEL 1 A, E, K, O Histone H3.2 8355
124 3KUY 1 A, E Histone H3.2 8355
125 4R8P 1 A, E Histone H3.2 8355
126 3AZM 1 A, E Histone H3.1 9606
127 3X1U 2 A, E Histone H3.1 9606
128 3MGS 1 A, E Histone H3.2 8355
129 3WA9 1 A, E Histone H3.1 9606
130 1ID3 2 A, E HISTONE H3 4932
131 3C1C 1 A, E Histone H3-like 8355
132 3AZH 1 A, E Histone H3.1 9606
133 5B40 1 A, E Histone H3.2 9606
134 3WAA 1 A, E Histone H3.1 9606
135 5CPI 1 A, E Histone H3.1 9606
136 4JJN 1 A, E Histone H3 4932
137 3W99 1 A, E Histone H3.1 9606
138 3AZE 1 A, E Histone H3.1 9606
139 3W96 1 A, E Histone H3.1 9606
140 5CPJ 1 A, E Histone H3.1 9606
141 5B24 1 A, E Histone H3.1 9606
142 5C3I 2 B, F, J, N, R, V Histone H3.1 9606
143 2HIO 3 C PROTEIN (HISTONE H3) 9031
144 4QLC 3 A, E Histone H3 7227
145 4LD9 1 A, E Histone H3.2 8355
146 3O62 1 A, E Histone H3.2 8355
147 4XUJ 1 A, E Histone H3.2 UNP residues 2-136 8355
148 5KDM 1 A Histone H3.3 9606
149 3W97 1 A, E Histone H3.1 9606
150 4YM5 1 A, E Histone H3.1 9606
151 4YM6 1 A, E Histone H3.1 9606
152 2FJ7 3 A, E histone H3 8355
153 4ZUX 1 A, E, K, O Histone H3.2 8355
154 3AN2 1 A, E Histone H3-like centromeric protein A 9606
155 3B6F 3 A, E Histone H3.2 8355
156 5OY7 2 A, E, I, M, Q, U, Y, c Histone H3 8355
157 3B6G 3 A, E Histone H3.2 8355
158 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
159 3KXB 1 A, E Histone H3.2 8355
160 5HQ2 1 A Histone H3.2 8355
161 5OXV 5 A, E, K, O Histone H3.2 8355
162 1ZBB 3 A, E, a, e HISTONE H3 8355
163 5O9G 1 A, E Histone H3.2 8355
164 5X0X 1 A, E Histone H3.2 8355
165 5X0Y 1 A, E Histone H3.2 8355
166 5KGF 1 A, E Histone H3.2 8355
167 3C9K 3 C, G Histone H3.2 9031