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 % 14 40 452
95 % 54 168 76 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 54 171 79
70 % 54 172 95
50 % 55 176 124
40 % 55 176 145
30 % 55 176 160
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 % 56 178 55
95 % 58 181 68 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 59 185 70
70 % 59 185 89
50 % 59 185 118
40 % 59 185 141
30 % 59 185 153
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 % 18 51 335
95 % 47 163 78 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.6
PDBFlex
90 % 49 171 74
70 % 51 177 90
50 % 56 187 109
40 % 56 187 132
30 % 56 187 145
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 % 18 53 294
95 % 46 157 89 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 46 157 92
70 % 49 169 100
50 % 49 169 134
40 % 49 169 150
30 % 49 169 169
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 2YFW 2 B, D, F, H HISTONE H4 28985
55 3REH 2 B, F Histone H4 8355
56 3AZL 2 B, F Histone H4 9606
57 3NQU 2 B Histone H4 9606
58 5BNV 2 B, E Histone H4 9606
59 3AFA 2 B, F Histone H4 9606
60 5E5A 3 B, F Histone H4 8355
61 3REJ 2 B, F Histone H4 8355
62 3AZF 2 B, F Histone H4 9606
63 5GTC 2 B, F Histone H4 9606
64 1P3P 3 B, F Histone H4 8355
65 3AV1 2 B, F Histone H4 9606
66 1M1A 3 B, F Histone H4 8355
67 5CPK 2 B, F Histone H4 9606
68 5AY8 2 B, F Histone H4 9606
69 3MNN 2 B, F Histone H4 8355
70 5BO0 2 B Histone H4 9606
71 1P3G 3 B, F Histone H4 8355
72 4J8W 2 B, F Histone H4 8355
73 1P34 3 B, F Histone H4 8355
74 5XF3 2 B, F Histone H4 9606
75 3X1V 3 B, F Histone H4 9606
76 5ONG 4 B, F Histone H4 8355
77 5ONW 4 B, F Histone H4 8355
78 5DNM 2 B, F Histone H4 8355
79 4HGA 3 C Histone H4 9606
80 4UUZ 2 B HISTONE H4 7227
81 3MGQ 2 B, F Histone H4 8355
82 3WTP 2 B, F Histone H4 9606
83 3X1T 3 B, F Histone H4 9606
84 2NZD 4 B, F Histone H4 8355
85 3A6N 2 B, F Histone H4 9606
86 5DNN 2 B, F Histone H4 8355
87 5GT3 2 B, F Histone H4 9606
88 5GT0 2 B, F Histone H4 9606
89 3LJA 2 B, F Histone H4 8355
90 3AZI 2 B, F Histone H4 9606
91 3TU4 2 B, F Histone H4 8355
92 1P3O 3 B, F Histone H4 8355
93 4Z2M 3 H, J Histone H4 9606
94 1KX4 3 B, F histone H4 8355
95 3AZN 2 B, F Histone H4 9606
96 1P3M 3 B, F Histone H4 8355
97 4J8V 2 B, F Histone H4 8355
98 5B33 2 B, F Histone H4 9606
99 3X1S 2 B, F Histone H4 9606
100 3LZ0 2 B, F Histone H4 8355
101 1P3F 3 B, F Histone H4 8355
102 1P3K 3 B, F Histone H4 8355
103 4XYI 2 B Histone H4 4897
104 5B2I 2 B, F Histone H4 9606
105 1P3A 3 B, F Histone H4 8355
106 3LZ1 2 B, F Histone H4 8355
107 2IO5 3 C Histone H4 8355
108 5GXQ 2 B, F Histone H4 9606
109 2F8N 3 B, F Histone H4 8355
110 4Z5T 2 B, F Histone H4 9606
111 1U35 3 B, F Hist1h4i protein 10090
112 5XM0 2 B, F Histone H4 10090
113 3AV2 2 B, F Histone H4 9606
114 3AYW 2 B, F Histone H4 9606
115 5XF5 2 B, F Histone H4 9606
116 3AZJ 2 B, F Histone H4 9606
117 3REK 2 B, F Histone H4 8355
118 4KGC 2 B, F Histone H4 8355
119 1ZLA 3 B, F Histone H4 8355
120 5GSU 2 B, F Histone H4 9606
121 5XF4 2 B, F Histone H4 9606
122 3REL 2 B, F Histone H4 8355
123 5GSE 2 B, F, L, P Histone H4 9606
124 3REI 2 B, F Histone H4 8355
125 1P3B 3 B, F Histone H4 8355
126 3WKJ 2 B, F Histone H4 9606
127 4KUD 2 B, F Histone H4 4932
128 3AZK 2 B, F Histone H4 9606
129 4J8X 2 B, F Histone H4 8355
130 3LEL 2 B, F, L, P Histone H4 8355
131 3KUY 2 B, F Histone H4 8355
132 4R8P 2 B, F Histone H4 8355
133 3AZM 2 B, F Histone H4 9606
134 3X1U 3 B, F Histone H4 9606
135 3MGS 2 B, F Histone H4 8355
136 3WA9 2 B, F Histone H4 9606
137 1ID3 3 B, F HISTONE H4 4932
138 3C1C 2 B, F Histone H4 8355
139 3AZH 2 B, F Histone H4 9606
140 5B40 2 B, F Histone H4 9606
141 3WAA 2 B, F Histone H4 9606
142 5CPI 2 B, F Histone H4 9606
143 4JJN 2 B, F Histone H4 4932
144 3AZE 2 B, F Histone H4 9606
145 3W96 2 B, F Histone H4 9606
146 5XM1 2 B, F Histone H4 10090
147 5CPJ 2 B, F Histone H4 9606
148 5B24 2 B, F Histone H4 9606
149 5BS7 2 C, D Histone H4 8355
150 5C3I 3 C, G, K, O, S, W Histone H4 9606
151 2HIO 4 D PROTEIN (HISTONE H4) 9031
152 4QLC 4 B, F Histone H4 7227
153 4LD9 2 B, F Histone H4 8355
154 3O62 2 B, F Histone H4 8355
155 4XUJ 2 B, F Histone H4 UNP residues 2-103 8355
156 5KDM 2 B Histone H4 9606
157 3W97 2 B, F Histone H4 9606
158 4YM5 2 B, F Histone H4 9606
159 4YM6 2 B, F Histone H4 9606
160 2FJ7 4 B, F Histone H4 8355
161 3W98 2 B, F Histone H4 9606
162 4ZUX 2 B, F, L, P Histone H4 8355
163 3AN2 2 B, F Histone H4 9606
164 5BSA 2 C, D Histone H4 8355
165 3B6F 4 B, F Histone H4 8355
166 5OY7 3 B, F, J, N, R, V, Z, d Histone H4 8355
167 3B6G 4 B, F Histone H4 8355
168 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
169 3KXB 2 B, F Histone H4 8355
170 5HQ2 2 B Histone H4 8355
171 5OXV 4 B, F, L, P Histone H4 8355
172 1ZBB 4 B, F, b, f Histone H4 8355
173 6FML 10 N, R Histone H4 9606
174 6C0W 2 B, F Histone H4 9606
175 6BUZ 2 B, F Histone H4 9606
176 6ETX 6 J, N Histone H4 9606
177 6ESF 2 B, F Histone H4 8355
178 6ESG 2 B, F Histone H4 8355
179 6ESH 2 B, F Histone H4 8355
180 6ESI 2 B, F Histone H4 8355
181 5O9G 2 B, F Histone H4 8355
182 5X0X 2 B, F Histone H4 8355
183 5X0Y 2 B, F Histone H4 8355
184 5KGF 2 B, F Histone H4 cysteine alkylation at position 20 8355
185 3C9K 4 D, H Histone H4 9031