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.

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Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 4CAY 1 A HISTONE H2A.Z GLOBULAR DOMAIN, RESIDUES 19-128 9606
2 4WNN 1 A, C, E, G Histone H2A.1 4932
3 1TZY 1 A, E Histone H2A-IV 9031
4 1KX5 5 C, G histone H2A.1 8355
5 2ARO 1 A, E Histone H2A-IV 9031
6 5B0Z 3 C, G Histone H2A type 1-B/E 9606
7 1S32 4 C, G histone H2A 8355
8 5AV8 3 C, G Histone H2A type 1-B/E 9606
9 1KX3 4 C, G histone H2A.1 8355
10 5AV9 3 C, G Histone H2A type 1-B/E 9606
11 5AV6 3 C, G Histone H2A type 1-B/E 9606
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
16 5B31 3 C Histone H2A type 1-B/E 9606
17 5B31 5 G Histone H2A.Z 9606
18 5B1L 3 C, G Histone H2A type 1 10090
19 3UTB 3 C, G Histone H2A 8355
20 1M19 4 C, G Histone H2A.1 8355
21 5AVB 3 C, G Histone H2A type 1-B/E 9606
22 5AVC 3 C, G Histone H2A type 1-B/E 9606
23 5AV5 3 C, G Histone H2A type 1-B/E 9606
24 3C1B 3 C, G Histone H2A type 1 8355
25 5B1M 3 C, G Histone H2A type 1 10090
26 2NQB 4 C, G Histone H2A 7227
27 5OMX 5 C, G Histone H2A 8355
28 5F99 3 C, G Histone H2A type 1 8355
29 5JRG 3 C, G Histone H2A type 1-B/E 9606
30 3UT9 3 C, G Histone H2A 8355
31 5B32 3 C Histone H2A type 1-B/E 9606
32 5B32 5 G Histone H2A.Z 9606
33 4WU8 5 C, G Histone H2A type 1 8355
34 1P3I 4 C, G Histone H2A 8355
35 3MGR 3 C, G Histone H2A UNP RESIDUES 2-120 8355
36 1F66 4 C, G HISTONE H2A.Z 9606
37 3AZG 3 C, G Histone H2A type 1-B/E 9606
38 5FUG 1 A, D, G, J HISTONE H2A.Z GLOBULAR DOMAIN 9606
39 1M18 4 C, G Histone H2A.1 8355
40 5B2J 3 C, G Histone H2A type 1-B/E 9606
41 2PYO 5 C, G Histone H2A 7227
42 1P3L 4 C, G Histone H2A 8355
43 1EQZ 2 A, E PROTEIN (HISTONE H2A) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
44 5B0Y 3 C, G Histone H2A type 1-B/E 9606
45 2CV5 4 C, G Histone H2A.a 9606
46 5CP6 5 C, G Histone H2A 8355
47 5BT1 2 C Histone H2A.1 4932
48 5XF6 3 C, G Histone H2A 8355
49 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355
50 3MVD 3 C, G Histone H2A 8355
51 4J8U 3 C, G Histone H2A type 1 8355
52 4WU9 3 C, G Histone H2A type 1 8355
53 3REH 3 C, G Histone H2A type 1 8355
54 3AZL 3 C, G Histone H2A type 1-B/E 9606
55 4XZQ 3 C, G Histone H2A residues 15-121 8355
56 3AFA 3 C, G Histone H2A type 1-B/E 9606
57 5E5A 4 C, G Histone H2A 8355
58 3REJ 3 C, G Histone H2A type 1 8355
59 3AZF 3 C, G Histone H2A type 1-B/E 9606
60 5GTC 3 C, G Histone H2A type 1-B/E 9606
61 1P3P 4 C, G Histone H2A 8355
62 3AV1 3 C, G Histone H2A type 1-B/E 9606
63 1M1A 4 C, G Histone H2A.1 8355
64 5CPK 3 C, G Histone H2A type 1-B/E 9606
65 5AY8 3 C, G Histone H2A type 1-B/E 9606
66 3MNN 3 C, G Histone H2A 8355
67 1P3G 4 C, G Histone H2A 8355
68 4J8W 3 C, G Histone H2A 8355
69 1P34 4 C, G Histone H2A 8355
70 5XF3 3 C, G Histone H2A type 1-B/E 9606
71 3X1V 4 C, G Histone H2A type 1-B/E 9606
72 5MLU 3 C, G Histone H2A type 1 8355
73 5ONG 5 C, G Histone H2A 8355
74 5ONW 5 C, G Histone H2A 8355
75 5DNM 3 C, G Histone H2A 8355
76 4Z66 3 C, G Histone H2A 8355
77 3MGQ 3 C, G Histone H2A UNP RESIDUES 2-120 8355
78 3WTP 3 C, G Histone H2A type 1-B/E 9606
79 3X1T 4 C, G Histone H2A 10090
80 2NZD 5 C, G histone H2A 8355
81 3A6N 3 C, G Histone H2A type 1-B/E 9606
82 5DNN 3 C, G Histone H2A 8355
83 5GT3 3 C, G Histone H2A type 1-D 9606
84 5GT0 3 C, G Histone H2A type 1-A 9606
85 3LJA 3 C, G Histone H2A 8355
86 3AZI 3 C, G Histone H2A type 1-B/E 9606
87 3TU4 3 C, G Histone H2A 8355
88 1P3O 4 C, G Histone H2A 8355
89 1KX4 4 C, G histone H2A.1 8355
90 3AZN 3 C, G Histone H2A type 1-B/E 9606
91 1P3M 4 C, G Histone H2A 8355
92 4J8V 3 C, G Histone H2A 8355
93 5B33 3 C, G Histone H2A.Z 9606
94 1AOI 4 C, G HISTONE H2A HISTONE H2A 8355
95 3X1S 3 C, G Histone H2A type 1-B/E 9606
96 3LZ0 3 C, G Histone H2A residues 2-120 8355
97 1P3F 4 C, G Histone H2A 8355
98 1P3K 4 C, G Histone H2A 8355
99 5B2I 3 C, G Histone H2A type 1-B/E 9606
100 1P3A 4 C, G Histone H2A 8355
101 3LZ1 3 C, G Histone H2A residues 2-120 8355
102 5GXQ 3 C, G Histone H2A type 1-B/E 9606
103 2F8N 6 G Core histone macro-H2A.1 residues 0-119 9606
104 2F8N 7 K Histone H2A type 1 10090
105 4Z5T 3 C, G Histone H2A type 1-B/E 9606
106 1U35 4 C, G H2A histone family 9606
107 5XM0 3 C, G Histone H2A type 1-B 10090
108 3AV2 3 C, G Histone H2A type 1-B/E 9606
109 3AYW 3 C, G Histone H2A type 1-B/E 9606
110 5XF5 3 C, G Histone H2A type 1-B/E 9606
111 3AZJ 3 C, G Histone H2A type 1-B/E 9606
112 3REK 3 C, G Histone H2A type1 8355
113 4KGC 3 C, G Histone H2A 8355
114 1ZLA 4 C, G Xenopus laevis-like histone H2A 263730
115 5GSU 3 C, G Histone H2A type 1-A 9606
116 5XF4 3 C, G Histone H2A type 1-B/E 9606
117 3REL 3 C, G Histone H2A 8355
118 5GSE 3 C, G, M Histone H2A type 1-B/E 9606
119 3REI 3 C, G Histone H2A type1 8355
120 1P3B 4 C, G Histone H2A 8355
121 3WKJ 3 C, G Histone H2A type 1-B/E 9606
122 4KUD 3 C, G Histone H2A.2 4932
123 3AZK 3 C, G Histone H2A type 1-B/E 9606
124 4J8X 3 C, G Histone H2A 8355
125 3LEL 3 C, G, M, Q Histone H2A 8355
126 4YS3 3 C, G Histone H2A residues 15-121 8355
127 3KUY 3 C, G Histone H2A 8355
128 4R8P 3 C, G Histone H2A 8355
129 3AZM 3 C, G Histone H2A type 1-B/E 9606
130 3X1U 4 C, G Histone H2A 10090
131 3MGS 3 C, G Histone H2A UNP RESIDUES 2-120 8355
132 3WA9 3 C, G Histone H2A.Z 9606
133 1ID3 4 C, G HISTONE H2A.1 4932
134 3C1C 3 C, G Histone H2A type 1 8355
135 3AZH 3 C, G Histone H2A type 1-B/E 9606
136 5B40 3 C, G Histone H2A type 1-B/E 9606
137 3WAA 3 C, G Histone H2A.V 9606
138 5CPI 3 C, G Histone H2A type 1-B/E 9606
139 4JJN 3 C, G Histone H2A.2 4932
140 3W99 3 C, G Histone H2A type 1-B/E 9606
141 3AZE 3 C, G Histone H2A type 1-B/E 9606
142 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606
143 5XM1 3 C, G Histone H2A type 1-B 10090
144 5CPJ 3 C, G Histone H2A type 1-B/E 9606
145 5B24 3 C, G Histone H2A type 1-B/E 9606
146 2HIO 1 A PROTEIN (HISTONE H2A) 9031
147 1HIO 1 A HISTONE H2A 9031
148 4QLC 5 C, G Histone H2A 7227
149 4LD9 3 C, G Histone H2A 8355
150 3O62 3 C, G Histone H2A type 1 8355
151 4XUJ 3 C, G Histone H2A UNP residues 2-126 8355
152 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227
153 3W97 3 C, G Histone H2A type 1-B/E 9606
154 4YM5 3 C, G Histone H2A type 1-B/E 9606
155 4YM6 3 C, G Histone H2A type 1-B/E 9606
156 2FJ7 5 C, G histone H2A 8355
157 3W98 3 C, G Histone H2A type 1-B/E 9606
158 4ZUX 3 C, G, M, Q Histone H2A type 1 8355
159 3AN2 3 C, G Histone H2A type 1-B/E 9606
160 3B6F 5 C, G Histone H2A 8355
161 5OY7 4 C, G, K, O, S, W, a, e Histone H2A 8355
162 3B6G 5 C, G Histone H2A 8355
163 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
164 3KXB 3 C, G Histone H2A 8355
165 3KWQ 3 C, G Histone H2A UNP residues 15-121 8355
166 5G2E 2 C, G, K, O, S, W HISTONE H2A TYPE 1 8355
167 5HQ2 3 G Histone H2A 8355
168 5OXV 3 C, G, M, Q Histone H2A 8355
169 1ZBB 5 C, G, c, g Histone H2A.1 8355
170 6FQ5 3 C, G Histone H2A 8355
171 6FQ6 3 C, G Histone H2A 8355
172 6FQ8 3 C, G Histone H2A 8355
173 6C0W 3 C, G Histone H2A 9606
174 6BUZ 3 C, G Histone H2A 9606
175 6ESF 3 C, G Histone H2A 8355
176 6ESG 3 C, G Histone H2A 8355
177 6ESH 3 C, G Histone H2A 8355
178 6ESI 3 C, G Histone H2A 8355
179 5O9G 3 C, G Histone H2A 8355
180 5X0X 3 C, G Histone H2A 8355
181 5X0Y 3 C, G Histone H2A 8355
182 5KGF 3 C, G Histone H2A type 1 Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin 9606
183 2RVQ 1 C Histone H2A type 1-B/E 9606
184 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031
185 3C9K 1 A, E Histone H2A-IV 9031