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 45 310
95 % 54 160 77 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 54 163 77
70 % 54 164 92
50 % 55 167 125
40 % 55 167 145
30 % 55 167 156
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 % 53 151 58
95 % 58 170 71 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 59 175 69
70 % 59 175 83
50 % 59 175 116
40 % 59 175 139
30 % 59 175 144
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 57 247
95 % 47 150 81 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.6
PDBFlex
90 % 49 158 79
70 % 51 164 89
50 % 56 174 111
40 % 56 174 135
30 % 56 174 141
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 52 263
95 % 46 146 85 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 46 151 85
70 % 49 158 98
50 % 49 158 136
40 % 49 158 151
30 % 49 158 161
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 4WNN 1 A, C, E, G Histone H2A.1 4932
2 1TZY 1 A, E Histone H2A-IV 9031
3 1KX5 5 C, G histone H2A.1 8355
4 2ARO 1 A, E Histone H2A-IV 9031
5 5B0Z 3 C, G Histone H2A type 1-B/E 9606
6 1S32 4 C, G histone H2A 8355
7 5AV8 3 C, G Histone H2A type 1-B/E 9606
8 1KX3 4 C, G histone H2A.1 8355
9 5AV9 3 C, G Histone H2A type 1-B/E 9606
10 5AV6 3 C, G Histone H2A type 1-B/E 9606
11 1HQ3 1 A, E HISTONE H2A-IV 9031
12 3UTA 3 C, G Histone H2A 8355
13 4KHA 2 B Histone H2A UNP residues 15-103 8355
14 5X7X 3 C, G Histone H2A type 1-B/E 9606
15 5B31 3 C Histone H2A type 1-B/E 9606
16 5B1L 3 C, G Histone H2A type 1 10090
17 3UTB 3 C, G Histone H2A 8355
18 1M19 4 C, G Histone H2A.1 8355
19 5AVB 3 C, G Histone H2A type 1-B/E 9606
20 5AVC 3 C, G Histone H2A type 1-B/E 9606
21 5AV5 3 C, G Histone H2A type 1-B/E 9606
22 3C1B 3 C, G Histone H2A type 1 8355
23 5B1M 3 C, G Histone H2A type 1 10090
24 2NQB 4 C, G Histone H2A 7227
25 5OMX 5 C, G Histone H2A 8355
26 5F99 3 C, G Histone H2A type 1 8355
27 5JRG 3 C, G Histone H2A type 1-B/E 9606
28 3UT9 3 C, G Histone H2A 8355
29 5B32 3 C Histone H2A type 1-B/E 9606
30 4WU8 5 C, G Histone H2A type 1 8355
31 1P3I 4 C, G Histone H2A 8355
32 3MGR 3 C, G Histone H2A UNP RESIDUES 2-120 8355
33 3AZG 3 C, G Histone H2A type 1-B/E 9606
34 1M18 4 C, G Histone H2A.1 8355
35 5B2J 3 C, G Histone H2A type 1-B/E 9606
36 2PYO 5 C, G Histone H2A 7227
37 1P3L 4 C, G Histone H2A 8355
38 1EQZ 2 A, E PROTEIN (HISTONE H2A) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
39 5B0Y 3 C, G Histone H2A type 1-B/E 9606
40 2CV5 4 C, G Histone H2A.a 9606
41 5CP6 5 C, G Histone H2A 8355
42 5BT1 2 C Histone H2A.1 4932
43 5XF6 3 C, G Histone H2A 8355
44 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355
45 3MVD 3 C, G Histone H2A 8355
46 4J8U 3 C, G Histone H2A type 1 8355
47 4WU9 3 C, G Histone H2A type 1 8355
48 3REH 3 C, G Histone H2A type 1 8355
49 3AZL 3 C, G Histone H2A type 1-B/E 9606
50 4XZQ 3 C, G Histone H2A residues 15-121 8355
51 3AFA 3 C, G Histone H2A type 1-B/E 9606
52 5E5A 4 C, G Histone H2A 8355
53 3REJ 3 C, G Histone H2A type 1 8355
54 3AZF 3 C, G Histone H2A type 1-B/E 9606
55 5GTC 3 C, G Histone H2A type 1-B/E 9606
56 1P3P 4 C, G Histone H2A 8355
57 3AV1 3 C, G Histone H2A type 1-B/E 9606
58 1M1A 4 C, G Histone H2A.1 8355
59 5CPK 3 C, G Histone H2A type 1-B/E 9606
60 5AY8 3 C, G Histone H2A type 1-B/E 9606
61 3MNN 3 C, G Histone H2A 8355
62 1P3G 4 C, G Histone H2A 8355
63 4J8W 3 C, G Histone H2A 8355
64 1P34 4 C, G Histone H2A 8355
65 5XF3 3 C, G Histone H2A type 1-B/E 9606
66 3X1V 4 C, G Histone H2A type 1-B/E 9606
67 5MLU 3 C, G Histone H2A type 1 8355
68 5ONG 5 C, G Histone H2A 8355
69 5ONW 5 C, G Histone H2A 8355
70 5DNM 3 C, G Histone H2A 8355
71 4Z66 3 C, G Histone H2A 8355
72 3MGQ 3 C, G Histone H2A UNP RESIDUES 2-120 8355
73 3WTP 3 C, G Histone H2A type 1-B/E 9606
74 3X1T 4 C, G Histone H2A 10090
75 2NZD 5 C, G histone H2A 8355
76 3A6N 3 C, G Histone H2A type 1-B/E 9606
77 5DNN 3 C, G Histone H2A 8355
78 5GT3 3 C, G Histone H2A type 1-D 9606
79 5GT0 3 C, G Histone H2A type 1-A 9606
80 3LJA 3 C, G Histone H2A 8355
81 3AZI 3 C, G Histone H2A type 1-B/E 9606
82 3TU4 3 C, G Histone H2A 8355
83 1P3O 4 C, G Histone H2A 8355
84 1KX4 4 C, G histone H2A.1 8355
85 3AZN 3 C, G Histone H2A type 1-B/E 9606
86 1P3M 4 C, G Histone H2A 8355
87 4J8V 3 C, G Histone H2A 8355
88 1AOI 4 C, G HISTONE H2A HISTONE H2A 8355
89 3X1S 3 C, G Histone H2A type 1-B/E 9606
90 3LZ0 3 C, G Histone H2A residues 2-120 8355
91 1P3F 4 C, G Histone H2A 8355
92 1P3K 4 C, G Histone H2A 8355
93 5B2I 3 C, G Histone H2A type 1-B/E 9606
94 1P3A 4 C, G Histone H2A 8355
95 3LZ1 3 C, G Histone H2A residues 2-120 8355
96 5GXQ 3 C, G Histone H2A type 1-B/E 9606
97 2F8N 7 K Histone H2A type 1 10090
98 4Z5T 3 C, G Histone H2A type 1-B/E 9606
99 3AV2 3 C, G Histone H2A type 1-B/E 9606
100 3AYW 3 C, G Histone H2A type 1-B/E 9606
101 5XF5 3 C, G Histone H2A type 1-B/E 9606
102 3AZJ 3 C, G Histone H2A type 1-B/E 9606
103 3REK 3 C, G Histone H2A type1 8355
104 4KGC 3 C, G Histone H2A 8355
105 1ZLA 4 C, G Xenopus laevis-like histone H2A 263730
106 5GSU 3 C, G Histone H2A type 1-A 9606
107 5XF4 3 C, G Histone H2A type 1-B/E 9606
108 3REL 3 C, G Histone H2A 8355
109 5GSE 3 C, G, M Histone H2A type 1-B/E 9606
110 3REI 3 C, G Histone H2A type1 8355
111 1P3B 4 C, G Histone H2A 8355
112 3WKJ 3 C, G Histone H2A type 1-B/E 9606
113 4KUD 3 C, G Histone H2A.2 4932
114 3AZK 3 C, G Histone H2A type 1-B/E 9606
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
121 3X1U 4 C, G Histone H2A 10090
122 3MGS 3 C, G Histone H2A UNP RESIDUES 2-120 8355
123 1ID3 4 C, G HISTONE H2A.1 4932
124 3C1C 3 C, G Histone H2A type 1 8355
125 3AZH 3 C, G Histone H2A type 1-B/E 9606
126 5B40 3 C, G Histone H2A type 1-B/E 9606
127 5CPI 3 C, G Histone H2A type 1-B/E 9606
128 4JJN 3 C, G Histone H2A.2 4932
129 3W99 3 C, G Histone H2A type 1-B/E 9606
130 3AZE 3 C, G Histone H2A type 1-B/E 9606
131 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606
132 5CPJ 3 C, G Histone H2A type 1-B/E 9606
133 5B24 3 C, G Histone H2A type 1-B/E 9606
134 2HIO 1 A PROTEIN (HISTONE H2A) 9031
135 1HIO 1 A HISTONE H2A 9031
136 4QLC 5 C, G Histone H2A 7227
137 4LD9 3 C, G Histone H2A 8355
138 3O62 3 C, G Histone H2A type 1 8355
139 4XUJ 3 C, G Histone H2A UNP residues 2-126 8355
140 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227
141 3W97 3 C, G Histone H2A type 1-B/E 9606
142 4YM5 3 C, G Histone H2A type 1-B/E 9606
143 4YM6 3 C, G Histone H2A type 1-B/E 9606
144 2FJ7 5 C, G histone H2A 8355
145 3W98 3 C, G Histone H2A type 1-B/E 9606
146 4ZUX 3 C, G, M, Q Histone H2A type 1 8355
147 3AN2 3 C, G Histone H2A type 1-B/E 9606
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 5OXV 3 C, G, M, Q Histone H2A 8355
157 1ZBB 5 C, G, c, g Histone H2A.1 8355
158 5O9G 3 C, G Histone H2A 8355
159 5X0X 3 C, G Histone H2A 8355
160 5X0Y 3 C, G Histone H2A 8355
161 5KGF 3 C, G Histone H2A type 1 Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin 9606
162 2RVQ 1 C Histone H2A type 1-B/E 9606
163 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031
164 3C9K 1 A, E Histone H2A-IV 9031