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 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
5 1S32 4 C, G histone H2A 8355
6 5AV8 3 C, G Histone H2A type 1-B/E 9606
7 1KX3 4 C, G histone H2A.1 8355
8 5AV9 3 C, G Histone H2A type 1-B/E 9606
9 5AV6 3 C, G Histone H2A type 1-B/E 9606
10 1HQ3 1 A, E HISTONE H2A-IV 9031
11 3UTA 3 C, G Histone H2A 8355
12 4KHA 2 B Histone H2A UNP residues 15-103 8355
13 5X7X 3 C, G Histone H2A type 1-B/E 9606
14 5B31 3 C Histone H2A type 1-B/E 9606
15 5B1L 3 C, G Histone H2A type 1 10090
16 3UTB 3 C, G Histone H2A 8355
17 1M19 4 C, G Histone H2A.1 8355
18 5AVB 3 C, G Histone H2A type 1-B/E 9606
19 5AVC 3 C, G Histone H2A type 1-B/E 9606
20 5AV5 3 C, G Histone H2A type 1-B/E 9606
21 3C1B 3 C, G Histone H2A type 1 8355
22 5B1M 3 C, G Histone H2A type 1 10090
23 2NQB 4 C, G Histone H2A 7227
24 5F99 3 C, G Histone H2A type 1 8355
25 5JRG 3 C, G Histone H2A type 1-B/E 9606
26 3UT9 3 C, G Histone H2A 8355
27 5B32 3 C Histone H2A type 1-B/E 9606
28 4WU8 5 C, G Histone H2A type 1 8355
29 1P3I 4 C, G Histone H2A 8355
30 3MGR 3 C, G Histone H2A UNP RESIDUES 2-120 8355
31 3AZG 3 C, G Histone H2A type 1-B/E 9606
32 1M18 4 C, G Histone H2A.1 8355
33 5B2J 3 C, G Histone H2A type 1-B/E 9606
34 2PYO 5 C, G Histone H2A 7227
35 1P3L 4 C, G Histone H2A 8355
36 1EQZ 2 A, E PROTEIN (HISTONE H2A) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
37 5B0Y 3 C, G Histone H2A type 1-B/E 9606
38 2CV5 4 C, G Histone H2A.a 9606
39 5CP6 5 C, G Histone H2A 8355
40 5XF6 3 C, G Histone H2A 8355
41 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355
42 3MVD 3 C, G Histone H2A 8355
43 4J8U 3 C, G Histone H2A type 1 8355
44 4WU9 3 C, G Histone H2A type 1 8355
45 3REH 3 C, G Histone H2A type 1 8355
46 3AZL 3 C, G Histone H2A type 1-B/E 9606
47 4XZQ 3 C, G Histone H2A residues 15-121 8355
48 3AFA 3 C, G Histone H2A type 1-B/E 9606
49 5E5A 4 C, G Histone H2A 8355
50 3REJ 3 C, G Histone H2A type 1 8355
51 3AZF 3 C, G Histone H2A type 1-B/E 9606
52 5GTC 3 C, G Histone H2A type 1-B/E 9606
53 1P3P 4 C, G Histone H2A 8355
54 3AV1 3 C, G Histone H2A type 1-B/E 9606
55 1M1A 4 C, G Histone H2A.1 8355
56 5CPK 3 C, G Histone H2A type 1-B/E 9606
57 5AY8 3 C, G Histone H2A type 1-B/E 9606
58 3MNN 3 C, G Histone H2A 8355
59 1P3G 4 C, G Histone H2A 8355
60 4J8W 3 C, G Histone H2A 8355
61 1P34 4 C, G Histone H2A 8355
62 5XF3 3 C, G Histone H2A type 1-B/E 9606
63 3X1V 4 C, G Histone H2A type 1-B/E 9606
64 5MLU 3 C, G Histone H2A type 1 8355
65 5DNM 3 C, G Histone H2A 8355
66 4Z66 3 C, G Histone H2A 8355
67 3MGQ 3 C, G Histone H2A UNP RESIDUES 2-120 8355
68 3WTP 3 C, G Histone H2A type 1-B/E 9606
69 3X1T 4 C, G Histone H2A 10090
70 2NZD 5 C, G histone H2A 8355
71 3A6N 3 C, G Histone H2A type 1-B/E 9606
72 5DNN 3 C, G Histone H2A 8355
73 5GT3 3 C, G Histone H2A type 1-D 9606
74 5GT0 3 C, G Histone H2A type 1-A 9606
75 3LJA 3 C, G Histone H2A 8355
76 3AZI 3 C, G Histone H2A type 1-B/E 9606
77 3TU4 3 C, G Histone H2A 8355
78 1P3O 4 C, G Histone H2A 8355
79 1KX4 4 C, G histone H2A.1 8355
80 3AZN 3 C, G Histone H2A type 1-B/E 9606
81 1P3M 4 C, G Histone H2A 8355
82 4J8V 3 C, G Histone H2A 8355
83 1AOI 4 C, G HISTONE H2A HISTONE H2A 8355
84 3X1S 3 C, G Histone H2A type 1-B/E 9606
85 3LZ0 3 C, G Histone H2A residues 2-120 8355
86 1P3F 4 C, G Histone H2A 8355
87 1P3K 4 C, G Histone H2A 8355
88 5B2I 3 C, G Histone H2A type 1-B/E 9606
89 1P3A 4 C, G Histone H2A 8355
90 3LZ1 3 C, G Histone H2A residues 2-120 8355
91 5GXQ 3 C, G Histone H2A type 1-B/E 9606
92 4Z5T 3 C, G Histone H2A type 1-B/E 9606
93 3AV2 3 C, G Histone H2A type 1-B/E 9606
94 3AYW 3 C, G Histone H2A type 1-B/E 9606
95 5XF5 3 C, G Histone H2A type 1-B/E 9606
96 3AZJ 3 C, G Histone H2A type 1-B/E 9606
97 3REK 3 C, G Histone H2A type1 8355
98 4KGC 3 C, G Histone H2A 8355
99 1ZLA 4 C, G Xenopus laevis-like histone H2A 263730
100 5GSU 3 C, G Histone H2A type 1-A 9606
101 5XF4 3 C, G Histone H2A type 1-B/E 9606
102 3REL 3 C, G Histone H2A 8355
103 5GSE 3 C, G, M Histone H2A type 1-B/E 9606
104 3REI 3 C, G Histone H2A type1 8355
105 1P3B 4 C, G Histone H2A 8355
106 3WKJ 3 C, G Histone H2A type 1-B/E 9606
107 3AZK 3 C, G Histone H2A type 1-B/E 9606
108 4J8X 3 C, G Histone H2A 8355
109 3LEL 3 C, G, M, Q Histone H2A 8355
110 4YS3 3 C, G Histone H2A residues 15-121 8355
111 3KUY 3 C, G Histone H2A 8355
112 4R8P 3 C, G Histone H2A 8355
113 3AZM 3 C, G Histone H2A type 1-B/E 9606
114 3X1U 4 C, G Histone H2A 10090
115 3MGS 3 C, G Histone H2A UNP RESIDUES 2-120 8355
116 3C1C 3 C, G Histone H2A type 1 8355
117 3AZH 3 C, G Histone H2A type 1-B/E 9606
118 5B40 3 C, G Histone H2A type 1-B/E 9606
119 5CPI 3 C, G Histone H2A type 1-B/E 9606
120 3W99 3 C, G Histone H2A type 1-B/E 9606
121 3AZE 3 C, G Histone H2A type 1-B/E 9606
122 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606
123 5CPJ 3 C, G Histone H2A type 1-B/E 9606
124 5B24 3 C, G Histone H2A type 1-B/E 9606
125 2HIO 1 A PROTEIN (HISTONE H2A) 9031
126 1HIO 1 A HISTONE H2A 9031
127 4QLC 5 C, G Histone H2A 7227
128 4LD9 3 C, G Histone H2A 8355
129 3O62 3 C, G Histone H2A type 1 8355
130 4XUJ 3 C, G Histone H2A UNP residues 2-126 8355
131 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227
132 3W97 3 C, G Histone H2A type 1-B/E 9606
133 4YM5 3 C, G Histone H2A type 1-B/E 9606
134 4YM6 3 C, G Histone H2A type 1-B/E 9606
135 2FJ7 5 C, G histone H2A 8355
136 3W98 3 C, G Histone H2A type 1-B/E 9606
137 4ZUX 3 C, G, M, Q Histone H2A type 1 8355
138 3AN2 3 C, G Histone H2A type 1-B/E 9606
139 3B6F 5 C, G Histone H2A 8355
140 5OY7 4 C, G, K, O, S, W, a, e Histone H2A 8355
141 3B6G 5 C, G Histone H2A 8355
142 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
143 3KXB 3 C, G Histone H2A 8355
144 3KWQ 3 C, G Histone H2A UNP residues 15-121 8355
145 5G2E 2 C, G, K, O, S, W HISTONE H2A TYPE 1 8355
146 5HQ2 3 G Histone H2A 8355
147 5OXV 3 C, G, M, Q Histone H2A 8355
148 1ZBB 5 C, G, c, g Histone H2A.1 8355
149 5O9G 3 C, G Histone H2A 8355
150 5X0X 3 C, G Histone H2A 8355
151 5X0Y 3 C, G Histone H2A 8355
152 5KGF 3 C, G Histone H2A type 1 Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin 9606
153 2RVQ 1 C Histone H2A type 1-B/E 9606
154 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031
155 3C9K 1 A, E Histone H2A-IV 9031