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 % 24 70 202
95 % 57 182 73 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.1
PDBFlex
90 % 57 189 77
70 % 59 192 88
50 % 60 196 116
40 % 60 196 139
30 % 60 196 153
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 % 61 195 53
95 % 63 198 67 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 64 206 67
70 % 64 206 81
50 % 64 206 110
40 % 64 206 130
30 % 64 206 144
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 % 22 72 208
95 % 50 179 74 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.5
PDBFlex
90 % 52 188 73
70 % 54 196 82
50 % 60 207 105
40 % 60 207 125
30 % 60 207 140
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 % 23 66 230
95 % 23 66 294 Flexibility: No
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 51 174 80
70 % 54 188 90
50 % 54 188 122
40 % 54 188 144
30 % 54 188 158
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 1 A, E Histone H2A-IV 9031
2 1KX5 5 C, G histone H2A.1 8355
3 2ARO 1 A, E Histone H2A-IV 9031
4 5B0Z 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
5 5Y0D 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
6 5Y0C 4 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
7 1S32 4 C, G histone H2A 8355
8 5AV8 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
9 1KX3 4 C, G histone H2A.1 8355
10 5AV9 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
11 5AV6 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
12 1HQ3 1 A, E HISTONE H2A-IV 9031
13 3UTA 3 C, G Histone H2A 8355
14 4KHA 2 B Histone H2A UNP residues 15-103 8355
15 5X7X 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
16 5B31 3 C Histone H2A type 1-B/E 9606 3.2.1.21 | Details
17 5B1L 3 C, G Histone H2A type 1 10090
18 3UTB 3 C, G Histone H2A 8355
19 1M19 4 C, G Histone H2A.1 8355
20 5AVB 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
21 5AVC 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
22 5AV5 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
23 3C1B 3 C, G Histone H2A type 1 8355
24 5B1M 3 C, G Histone H2A type 1 10090
25 2NQB 4 C, G Histone H2A 7227
26 5OMX 5 C, G Histone H2A 8355
27 5F99 3 C, G Histone H2A type 1 8355
28 5JRG 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
29 3UT9 3 C, G Histone H2A 8355
30 5B32 3 C Histone H2A type 1-B/E 9606 3.2.1.21 | Details
31 4WU8 5 C, G Histone H2A type 1 8355
32 1P3I 4 C, G Histone H2A 8355
33 3MGR 3 C, G Histone H2A UNP RESIDUES 2-120 8355
34 3AZG 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
35 1M18 4 C, G Histone H2A.1 8355
36 5B2J 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
37 2PYO 5 C, G Histone H2A 7227
38 1P3L 4 C, G Histone H2A 8355
39 1EQZ 2 A, E PROTEIN (HISTONE H2A) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
40 5B0Y 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
41 2CV5 4 C, G Histone H2A.a 9606 3.2.1.21 | Details
42 5CP6 5 C, G Histone H2A 8355
43 5ZBX 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
44 5XF6 3 C, G Histone H2A 8355
45 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355
46 3MVD 3 C, G Histone H2A 8355
47 4J8U 3 C, G Histone H2A type 1 8355
48 4WU9 3 C, G Histone H2A type 1 8355
49 3REH 3 C, G Histone H2A type 1 8355
50 3AZL 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
51 4XZQ 3 C, G Histone H2A residues 15-121 8355
52 3AFA 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
53 5E5A 4 C, G Histone H2A 8355
54 3REJ 3 C, G Histone H2A type 1 8355
55 3AZF 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
56 5GTC 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
57 1P3P 4 C, G Histone H2A 8355
58 3AV1 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
59 1M1A 4 C, G Histone H2A.1 8355
60 5CPK 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
61 5AY8 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
62 3MNN 3 C, G Histone H2A 8355
63 1P3G 4 C, G Histone H2A 8355
64 4J8W 3 C, G Histone H2A 8355
65 1P34 4 C, G Histone H2A 8355
66 5XF3 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
67 3X1V 4 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
68 5MLU 3 C, G Histone H2A type 1 8355
69 5ONG 5 C, G Histone H2A 8355
70 5ONW 5 C, G Histone H2A 8355
71 5DNM 3 C, G Histone H2A 8355
72 4Z66 3 C, G Histone H2A 8355
73 3MGQ 3 C, G Histone H2A UNP RESIDUES 2-120 8355
74 3WTP 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
75 3X1T 4 C, G Histone H2A 10090
76 2NZD 5 C, G histone H2A 8355
77 3A6N 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
78 5DNN 3 C, G Histone H2A 8355
79 5GT3 3 C, G Histone H2A type 1-D 9606
80 5GT0 3 C, G Histone H2A type 1-A 9606
81 3LJA 3 C, G Histone H2A 8355
82 3AZI 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
83 3TU4 3 C, G Histone H2A 8355
84 1P3O 4 C, G Histone H2A 8355
85 1KX4 4 C, G histone H2A.1 8355
86 3AZN 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
87 1P3M 4 C, G Histone H2A 8355
88 4J8V 3 C, G Histone H2A 8355
89 1AOI 4 C, G HISTONE H2A HISTONE H2A 8355
90 3X1S 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
91 3LZ0 3 C, G Histone H2A residues 2-120 8355
92 1P3F 4 C, G Histone H2A 8355
93 1P3K 4 C, G Histone H2A 8355
94 5B2I 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
95 1P3A 4 C, G Histone H2A 8355
96 3LZ1 3 C, G Histone H2A residues 2-120 8355
97 5GXQ 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
98 4Z5T 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
99 5XM0 3 C, G Histone H2A type 1-B 10090
100 3AV2 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
101 3AYW 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
102 5XF5 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
103 3AZJ 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
104 3REK 3 C, G Histone H2A type1 8355
105 4KGC 3 C, G Histone H2A 8355
106 1ZLA 4 C, G Xenopus laevis-like histone H2A 263730
107 5GSU 3 C, G Histone H2A type 1-A 9606
108 5XF4 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
109 3REL 3 C, G Histone H2A 8355
110 5GSE 3 C, G, M Histone H2A type 1-B/E 9606 3.2.1.21 | Details
111 3REI 3 C, G Histone H2A type1 8355
112 1P3B 4 C, G Histone H2A 8355
113 3WKJ 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
114 3AZK 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
115 4J8X 3 C, G Histone H2A 8355
116 3LEL 3 C, G, M, Q Histone H2A 8355
117 4YS3 3 C, G Histone H2A residues 15-121 8355
118 3KUY 3 C, G Histone H2A 8355
119 4R8P 3 C, G Histone H2A 8355
120 3AZM 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
121 3X1U 4 C, G Histone H2A 10090
122 3MGS 3 C, G Histone H2A UNP RESIDUES 2-120 8355
123 3C1C 3 C, G Histone H2A type 1 8355
124 3AZH 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
125 5B40 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
126 5CPI 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
127 3W99 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
128 3AZE 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
129 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606 3.2.1.21 | Details
130 5XM1 3 C, G Histone H2A type 1-B 10090
131 5CPJ 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
132 5B24 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
133 2HIO 1 A PROTEIN (HISTONE H2A) 9031
134 1HIO 1 A HISTONE H2A 9031
135 4QLC 5 C, G Histone H2A 7227
136 4LD9 3 C, G Histone H2A 8355
137 3O62 3 C, G Histone H2A type 1 8355
138 4XUJ 3 C, G Histone H2A UNP residues 2-126 8355
139 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227
140 3W97 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
141 4YM5 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
142 4YM6 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
143 2FJ7 5 C, G histone H2A 8355
144 3W98 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
145 4ZUX 3 C, G, M, Q Histone H2A type 1 8355
146 3AN2 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
147 5WCU 3 C, G, M, Q Histone H2A UNP residues 15-118 7227
148 3B6F 5 C, G Histone H2A 8355
149 5OY7 4 C, G, K, O, S, W, a, e Histone H2A 8355
150 3B6G 5 C, G Histone H2A 8355
151 5NL0 3 C, G, M Histone H2A type 1 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
152 3KXB 3 C, G Histone H2A 8355
153 3KWQ 3 C, G Histone H2A UNP residues 15-121 8355
154 5G2E 2 C, G, K, O, S, W HISTONE H2A TYPE 1 8355
155 5HQ2 3 G Histone H2A 8355
156 6HKT 3 0, 2, C, G, M, Q, W, c, g, m, q, w Histone H2A type 1-B/E THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG 9606 3.2.1.21 | Details
157 5OXV 3 C, G, M, Q Histone H2A 8355
158 1ZBB 5 C, G, c, g Histone H2A.1 8355
159 6NN6 3 C, G Histone H2A type 1 8355
160 6I84 2 Q, V Histone H2A type 1 8355
161 6HTS 7 K, O Histone H2A type 1-B/E 9606 3.2.1.21 | Details
162 6A5O 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
163 6A5P 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
164 6A5R 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
165 6A5T 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
166 6A5U 18 c, g Histone H2A, Histone H2A type 1-B/E 9606 3.2.1.21 | Details
167 6A5V 18 c, g Histone H2A, Histone H2A type 1-B/E 9606 3.2.1.21 | Details
168 6A5L 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
169 6G0L 3 C Histone H2A type 1 8355
170 6G0L 5 G Histone H2A type 1 8355
171 6FTX 3 C, G Histone H2A type 1 8355
172 6FQ5 3 C, G Histone H2A 8355
173 6FQ6 3 C, G Histone H2A 8355
174 6FQ8 3 C, G Histone H2A 8355
175 6FML 11 O, S Histone H2A type 1 9606
176 6C0W 3 C, G Histone H2A 9606
177 6BUZ 3 C, G Histone H2A 9606 3.2.1.21 | Details
178 6ESF 3 C, G Histone H2A 8355
179 6ESG 3 C, G Histone H2A 8355
180 6ESH 3 C, G Histone H2A 8355
181 6ESI 3 C, G Histone H2A 8355
182 5O9G 3 C, G Histone H2A 8355
183 5X0X 3 C, G Histone H2A 8355
184 5X0Y 3 C, G Histone H2A 8355
185 5KGF 3 C, G Histone H2A type 1 Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin 9606
186 2RVQ 1 C Histone H2A type 1-B/E 9606 3.2.1.21 | Details
187 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031
188 3C9K 1 A, E Histone H2A-IV 9031