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 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 5F99 2 B, F Histone H4 8355
31 5JRG 2 B, F Histone H4 9606
32 3UT9 2 B, F Histone H4 8355
33 5B32 2 B, F Histone H4 9606
34 3R45 2 B Histone H4 9606
35 4WU8 4 B, F Histone H4 8355
36 1P3I 3 B, F Histone H4 8355
37 3MGR 2 B, F Histone H4 8355
38 1F66 3 B, F HISTONE H4 10090
39 3AZG 2 B, F Histone H4 9606
40 1M18 3 B, F Histone H4 8355
41 5B2J 2 B, F Histone H4 9606
42 2PYO 4 B, F Histone H4 7227
43 1P3L 3 B, F Histone H4 8355
44 1EQZ 5 D, H PROTEIN (HISTONE H4) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
45 5B0Y 2 B, F Histone H4 9606
46 2CV5 3 B, F Histone H4 9606
47 5CP6 4 B, F Histone H4 8355
48 5XF6 2 B, F Histone H4 8355
49 3MGP 2 B, F Histone H4 8355
50 3MVD 2 B, F Histone H4 8355
51 4J8U 2 B, F Histone H4 8355
52 4WU9 2 B, F Histone H4 8355
53 2YFW 2 B, D, F, H HISTONE H4 28985
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 5DNM 2 B, F Histone H4 8355
76 4HGA 3 C Histone H4 9606
77 4UUZ 2 B HISTONE H4 7227
78 3MGQ 2 B, F Histone H4 8355
79 3WTP 2 B, F Histone H4 9606
80 3X1T 3 B, F Histone H4 9606
81 2NZD 4 B, F Histone H4 8355
82 3A6N 2 B, F Histone H4 9606
83 5DNN 2 B, F Histone H4 8355
84 5GT3 2 B, F Histone H4 9606
85 5GT0 2 B, F Histone H4 9606
86 3LJA 2 B, F Histone H4 8355
87 3AZI 2 B, F Histone H4 9606
88 3TU4 2 B, F Histone H4 8355
89 1P3O 3 B, F Histone H4 8355
90 4Z2M 3 H, J Histone H4 9606
91 1KX4 3 B, F histone H4 8355
92 3AZN 2 B, F Histone H4 9606
93 1P3M 3 B, F Histone H4 8355
94 4J8V 2 B, F Histone H4 8355
95 5B33 2 B, F Histone H4 9606
96 3X1S 2 B, F Histone H4 9606
97 3LZ0 2 B, F Histone H4 8355
98 1P3F 3 B, F Histone H4 8355
99 1P3K 3 B, F Histone H4 8355
100 4XYI 2 B Histone H4 4897
101 5B2I 2 B, F Histone H4 9606
102 1P3A 3 B, F Histone H4 8355
103 3LZ1 2 B, F Histone H4 8355
104 2IO5 3 C Histone H4 8355
105 5GXQ 2 B, F Histone H4 9606
106 2F8N 3 B, F Histone H4 8355
107 4Z5T 2 B, F Histone H4 9606
108 1U35 3 B, F Hist1h4i protein 10090
109 3AV2 2 B, F Histone H4 9606
110 3AYW 2 B, F Histone H4 9606
111 5XF5 2 B, F Histone H4 9606
112 3AZJ 2 B, F Histone H4 9606
113 3REK 2 B, F Histone H4 8355
114 4KGC 2 B, F Histone H4 8355
115 1ZLA 3 B, F Histone H4 8355
116 5GSU 2 B, F Histone H4 9606
117 5XF4 2 B, F Histone H4 9606
118 3REL 2 B, F Histone H4 8355
119 5GSE 2 B, F, L, P Histone H4 9606
120 3REI 2 B, F Histone H4 8355
121 1P3B 3 B, F Histone H4 8355
122 3WKJ 2 B, F Histone H4 9606
123 4KUD 2 B, F Histone H4 4932
124 3AZK 2 B, F Histone H4 9606
125 4J8X 2 B, F Histone H4 8355
126 3LEL 2 B, F, L, P Histone H4 8355
127 3KUY 2 B, F Histone H4 8355
128 4R8P 2 B, F Histone H4 8355
129 3AZM 2 B, F Histone H4 9606
130 3X1U 3 B, F Histone H4 9606
131 3MGS 2 B, F Histone H4 8355
132 3WA9 2 B, F Histone H4 9606
133 1ID3 3 B, F HISTONE H4 4932
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 4JJN 2 B, F Histone H4 4932
140 3AZE 2 B, F Histone H4 9606
141 3W96 2 B, F Histone H4 9606
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 5O9G 2 B, F Histone H4 8355
169 5X0X 2 B, F Histone H4 8355
170 5X0Y 2 B, F Histone H4 8355
171 5KGF 2 B, F Histone H4 cysteine alkylation at position 20 8355
172 3C9K 4 D, H Histone H4 9031