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 45 337
95 % 54 166 77 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 54 169 80
70 % 54 170 94
50 % 55 174 124
40 % 55 174 144
30 % 55 174 151
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 % 53 159 57
95 % 58 178 68 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 59 183 70
70 % 59 183 86
50 % 59 183 115
40 % 59 183 139
30 % 59 183 144
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 60 241
95 % 47 161 78 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.6
PDBFlex
90 % 49 169 75
70 % 51 175 89
50 % 56 185 108
40 % 56 185 130
30 % 56 185 139
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 53 285
95 % 46 155 89 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 46 160 86
70 % 49 167 99
50 % 49 167 136
40 % 49 167 149
30 % 49 167 159
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.

You can also use the structure comparison tool to compare any 2 given structures


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 4 D, H HISTONE H4-VI 9031
2 4H9N 2 B Histone H4 9606
3 4H9Q 2 B Histone H4 9606
4 1KX5 4 B, F histone H4 8355
5 4H9O 2 B Histone H4 9606
6 2ARO 4 D, H HISTONE H4-VI 9031
7 5B0Z 2 B, F Histone H4 9606
8 4H9R 2 B Histone H4 9606
9 1S32 3 B, F Histone H4 8355
10 4H9P 2 B Histone H4 9606
11 5AV8 2 B, F Histone H4 9606
12 1KX3 3 B, F histone H4 8355
13 5AV9 2 B, F Histone H4 9606
14 5AV6 2 B, F Histone H4 9606
15 1HQ3 4 D, H HISTONE H4-VI 9031
16 5BNX 2 B Histone H4 9606
17 3UTA 2 B, F Histone H4 8355
18 5X7X 2 B, F Histone H4 9606
19 5B31 2 B, F Histone H4 9606
20 5B1L 2 B, F Histone H4 10090
21 3UTB 2 B, F Histone H4 8355
22 1M19 3 B, F Histone H4 8355
23 5AVB 2 B, F Histone H4 9606
24 5AVC 2 B, F Histone H4 9606
25 5AV5 2 B, F Histone H4 9606
26 3C1B 2 B, F Histone H4 8355
27 5B1M 2 B, F Histone H4 10090
28 2NQB 3 B, F Histone H4 7227
29 5JA4 2 B Histone H4 9606
30 5OMX 4 B, F Histone H4 8355
31 5F99 2 B, F Histone H4 8355
32 5JRG 2 B, F Histone H4 9606
33 3UT9 2 B, F Histone H4 8355
34 5B32 2 B, F Histone H4 9606
35 3R45 2 B Histone H4 9606
36 4WU8 4 B, F Histone H4 8355
37 1P3I 3 B, F Histone H4 8355
38 3MGR 2 B, F Histone H4 8355
39 1F66 3 B, F HISTONE H4 10090
40 3AZG 2 B, F Histone H4 9606
41 1M18 3 B, F Histone H4 8355
42 5B2J 2 B, F Histone H4 9606
43 2PYO 4 B, F Histone H4 7227
44 1P3L 3 B, F Histone H4 8355
45 1EQZ 5 D, H PROTEIN (HISTONE H4) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
46 5B0Y 2 B, F Histone H4 9606
47 2CV5 3 B, F Histone H4 9606
48 5CP6 4 B, F Histone H4 8355
49 5XF6 2 B, F Histone H4 8355
50 3MGP 2 B, F Histone H4 8355
51 3MVD 2 B, F Histone H4 8355
52 4J8U 2 B, F Histone H4 8355
53 4WU9 2 B, F Histone H4 8355
54 3REH 2 B, F Histone H4 8355
55 3AZL 2 B, F Histone H4 9606
56 3NQU 2 B Histone H4 9606
57 5BNV 2 B, E Histone H4 9606
58 3AFA 2 B, F Histone H4 9606
59 5E5A 3 B, F Histone H4 8355
60 3REJ 2 B, F Histone H4 8355
61 3AZF 2 B, F Histone H4 9606
62 5GTC 2 B, F Histone H4 9606
63 1P3P 3 B, F Histone H4 8355
64 3AV1 2 B, F Histone H4 9606
65 1M1A 3 B, F Histone H4 8355
66 5CPK 2 B, F Histone H4 9606
67 5AY8 2 B, F Histone H4 9606
68 3MNN 2 B, F Histone H4 8355
69 5BO0 2 B Histone H4 9606
70 1P3G 3 B, F Histone H4 8355
71 4J8W 2 B, F Histone H4 8355
72 1P34 3 B, F Histone H4 8355
73 5XF3 2 B, F Histone H4 9606
74 3X1V 3 B, F Histone H4 9606
75 5ONG 4 B, F Histone H4 8355
76 5ONW 4 B, F Histone H4 8355
77 5DNM 2 B, F Histone H4 8355
78 4HGA 3 C Histone H4 9606
79 4UUZ 2 B HISTONE H4 7227
80 3MGQ 2 B, F Histone H4 8355
81 3WTP 2 B, F Histone H4 9606
82 3X1T 3 B, F Histone H4 9606
83 2NZD 4 B, F Histone H4 8355
84 3A6N 2 B, F Histone H4 9606
85 5DNN 2 B, F Histone H4 8355
86 5GT3 2 B, F Histone H4 9606
87 5GT0 2 B, F Histone H4 9606
88 3LJA 2 B, F Histone H4 8355
89 3AZI 2 B, F Histone H4 9606
90 3TU4 2 B, F Histone H4 8355
91 1P3O 3 B, F Histone H4 8355
92 4Z2M 3 H, J Histone H4 9606
93 1KX4 3 B, F histone H4 8355
94 3AZN 2 B, F Histone H4 9606
95 1P3M 3 B, F Histone H4 8355
96 4J8V 2 B, F Histone H4 8355
97 5B33 2 B, F Histone H4 9606
98 3X1S 2 B, F Histone H4 9606
99 3LZ0 2 B, F Histone H4 8355
100 1P3F 3 B, F Histone H4 8355
101 1P3K 3 B, F Histone H4 8355
102 5B2I 2 B, F Histone H4 9606
103 1P3A 3 B, F Histone H4 8355
104 3LZ1 2 B, F Histone H4 8355
105 2IO5 3 C Histone H4 8355
106 5GXQ 2 B, F Histone H4 9606
107 2F8N 3 B, F Histone H4 8355
108 4Z5T 2 B, F Histone H4 9606
109 1U35 3 B, F Hist1h4i protein 10090
110 5XM0 2 B, F Histone H4 10090
111 3AV2 2 B, F Histone H4 9606
112 3AYW 2 B, F Histone H4 9606
113 5XF5 2 B, F Histone H4 9606
114 3AZJ 2 B, F Histone H4 9606
115 3REK 2 B, F Histone H4 8355
116 4KGC 2 B, F Histone H4 8355
117 1ZLA 3 B, F Histone H4 8355
118 5GSU 2 B, F Histone H4 9606
119 5XF4 2 B, F Histone H4 9606
120 3REL 2 B, F Histone H4 8355
121 5GSE 2 B, F, L, P Histone H4 9606
122 3REI 2 B, F Histone H4 8355
123 1P3B 3 B, F Histone H4 8355
124 3WKJ 2 B, F Histone H4 9606
125 3AZK 2 B, F Histone H4 9606
126 4J8X 2 B, F Histone H4 8355
127 3LEL 2 B, F, L, P Histone H4 8355
128 3KUY 2 B, F Histone H4 8355
129 4R8P 2 B, F Histone H4 8355
130 3AZM 2 B, F Histone H4 9606
131 3X1U 3 B, F Histone H4 9606
132 3MGS 2 B, F Histone H4 8355
133 3WA9 2 B, F Histone H4 9606
134 3C1C 2 B, F Histone H4 8355
135 3AZH 2 B, F Histone H4 9606
136 5B40 2 B, F Histone H4 9606
137 3WAA 2 B, F Histone H4 9606
138 5CPI 2 B, F Histone H4 9606
139 3AZE 2 B, F Histone H4 9606
140 3W96 2 B, F Histone H4 9606
141 5XM1 2 B, F Histone H4 10090
142 5CPJ 2 B, F Histone H4 9606
143 5B24 2 B, F Histone H4 9606
144 5BS7 2 C, D Histone H4 8355
145 5C3I 3 C, G, K, O, S, W Histone H4 9606
146 2HIO 4 D PROTEIN (HISTONE H4) 9031
147 4QLC 4 B, F Histone H4 7227
148 4LD9 2 B, F Histone H4 8355
149 3O62 2 B, F Histone H4 8355
150 4XUJ 2 B, F Histone H4 UNP residues 2-103 8355
151 5KDM 2 B Histone H4 9606
152 3W97 2 B, F Histone H4 9606
153 4YM5 2 B, F Histone H4 9606
154 4YM6 2 B, F Histone H4 9606
155 2FJ7 4 B, F Histone H4 8355
156 3W98 2 B, F Histone H4 9606
157 4ZUX 2 B, F, L, P Histone H4 8355
158 3AN2 2 B, F Histone H4 9606
159 5BSA 2 C, D Histone H4 8355
160 3B6F 4 B, F Histone H4 8355
161 5OY7 3 B, F, J, N, R, V, Z, d Histone H4 8355
162 3B6G 4 B, F Histone H4 8355
163 5NL0 2 B, F, L Histone H4 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
164 3KXB 2 B, F Histone H4 8355
165 5HQ2 2 B Histone H4 8355
166 5OXV 4 B, F, L, P Histone H4 8355
167 1ZBB 4 B, F, b, f Histone H4 8355
168 6C0W 2 B, F Histone H4 9606
169 6BUZ 2 B, F Histone H4 9606
170 6ESF 2 B, F Histone H4 8355
171 6ESG 2 B, F Histone H4 8355
172 6ESH 2 B, F Histone H4 8355
173 6ESI 2 B, F Histone H4 8355
174 5O9G 2 B, F Histone H4 8355
175 5X0X 2 B, F Histone H4 8355
176 5X0Y 2 B, F Histone H4 8355
177 5KGF 2 B, F Histone H4 cysteine alkylation at position 20 8355
178 3C9K 4 D, H Histone H4 9031