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 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 5F99 3 C, G Histone H2A type 1 8355
26 5JRG 3 C, G Histone H2A type 1-B/E 9606
27 3UT9 3 C, G Histone H2A 8355
28 5B32 3 C Histone H2A type 1-B/E 9606
29 4WU8 5 C, G Histone H2A type 1 8355
30 1P3I 4 C, G Histone H2A 8355
31 3MGR 3 C, G Histone H2A UNP RESIDUES 2-120 8355
32 3AZG 3 C, G Histone H2A type 1-B/E 9606
33 1M18 4 C, G Histone H2A.1 8355
34 5B2J 3 C, G Histone H2A type 1-B/E 9606
35 2PYO 5 C, G Histone H2A 7227
36 1P3L 4 C, G Histone H2A 8355
37 1EQZ 2 A, E PROTEIN (HISTONE H2A) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
38 5B0Y 3 C, G Histone H2A type 1-B/E 9606
39 2CV5 4 C, G Histone H2A.a 9606
40 5CP6 5 C, G Histone H2A 8355
41 5BT1 2 C Histone H2A.1 4932
42 5XF6 3 C, G Histone H2A 8355
43 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355
44 3MVD 3 C, G Histone H2A 8355
45 4J8U 3 C, G Histone H2A type 1 8355
46 4WU9 3 C, G Histone H2A type 1 8355
47 3REH 3 C, G Histone H2A type 1 8355
48 3AZL 3 C, G Histone H2A type 1-B/E 9606
49 4XZQ 3 C, G Histone H2A residues 15-121 8355
50 3AFA 3 C, G Histone H2A type 1-B/E 9606
51 5E5A 4 C, G Histone H2A 8355
52 3REJ 3 C, G Histone H2A type 1 8355
53 3AZF 3 C, G Histone H2A type 1-B/E 9606
54 5GTC 3 C, G Histone H2A type 1-B/E 9606
55 1P3P 4 C, G Histone H2A 8355
56 3AV1 3 C, G Histone H2A type 1-B/E 9606
57 1M1A 4 C, G Histone H2A.1 8355
58 5CPK 3 C, G Histone H2A type 1-B/E 9606
59 5AY8 3 C, G Histone H2A type 1-B/E 9606
60 3MNN 3 C, G Histone H2A 8355
61 1P3G 4 C, G Histone H2A 8355
62 4J8W 3 C, G Histone H2A 8355
63 1P34 4 C, G Histone H2A 8355
64 5XF3 3 C, G Histone H2A type 1-B/E 9606
65 3X1V 4 C, G Histone H2A type 1-B/E 9606
66 5MLU 3 C, G Histone H2A type 1 8355
67 5DNM 3 C, G Histone H2A 8355
68 4Z66 3 C, G Histone H2A 8355
69 3MGQ 3 C, G Histone H2A UNP RESIDUES 2-120 8355
70 3WTP 3 C, G Histone H2A type 1-B/E 9606
71 3X1T 4 C, G Histone H2A 10090
72 2NZD 5 C, G histone H2A 8355
73 3A6N 3 C, G Histone H2A type 1-B/E 9606
74 5DNN 3 C, G Histone H2A 8355
75 5GT3 3 C, G Histone H2A type 1-D 9606
76 5GT0 3 C, G Histone H2A type 1-A 9606
77 3LJA 3 C, G Histone H2A 8355
78 3AZI 3 C, G Histone H2A type 1-B/E 9606
79 3TU4 3 C, G Histone H2A 8355
80 1P3O 4 C, G Histone H2A 8355
81 1KX4 4 C, G histone H2A.1 8355
82 3AZN 3 C, G Histone H2A type 1-B/E 9606
83 1P3M 4 C, G Histone H2A 8355
84 4J8V 3 C, G Histone H2A 8355
85 1AOI 4 C, G HISTONE H2A HISTONE H2A 8355
86 3X1S 3 C, G Histone H2A type 1-B/E 9606
87 3LZ0 3 C, G Histone H2A residues 2-120 8355
88 1P3F 4 C, G Histone H2A 8355
89 1P3K 4 C, G Histone H2A 8355
90 5B2I 3 C, G Histone H2A type 1-B/E 9606
91 1P3A 4 C, G Histone H2A 8355
92 3LZ1 3 C, G Histone H2A residues 2-120 8355
93 5GXQ 3 C, G Histone H2A type 1-B/E 9606
94 2F8N 7 K Histone H2A type 1 10090
95 4Z5T 3 C, G Histone H2A type 1-B/E 9606
96 3AV2 3 C, G Histone H2A type 1-B/E 9606
97 3AYW 3 C, G Histone H2A type 1-B/E 9606
98 5XF5 3 C, G Histone H2A type 1-B/E 9606
99 3AZJ 3 C, G Histone H2A type 1-B/E 9606
100 3REK 3 C, G Histone H2A type1 8355
101 4KGC 3 C, G Histone H2A 8355
102 1ZLA 4 C, G Xenopus laevis-like histone H2A 263730
103 5GSU 3 C, G Histone H2A type 1-A 9606
104 5XF4 3 C, G Histone H2A type 1-B/E 9606
105 3REL 3 C, G Histone H2A 8355
106 5GSE 3 C, G, M Histone H2A type 1-B/E 9606
107 3REI 3 C, G Histone H2A type1 8355
108 1P3B 4 C, G Histone H2A 8355
109 3WKJ 3 C, G Histone H2A type 1-B/E 9606
110 4KUD 3 C, G Histone H2A.2 4932
111 3AZK 3 C, G Histone H2A type 1-B/E 9606
112 4J8X 3 C, G Histone H2A 8355
113 3LEL 3 C, G, M, Q Histone H2A 8355
114 4YS3 3 C, G Histone H2A residues 15-121 8355
115 3KUY 3 C, G Histone H2A 8355
116 4R8P 3 C, G Histone H2A 8355
117 3AZM 3 C, G Histone H2A type 1-B/E 9606
118 3X1U 4 C, G Histone H2A 10090
119 3MGS 3 C, G Histone H2A UNP RESIDUES 2-120 8355
120 1ID3 4 C, G HISTONE H2A.1 4932
121 3C1C 3 C, G Histone H2A type 1 8355
122 3AZH 3 C, G Histone H2A type 1-B/E 9606
123 5B40 3 C, G Histone H2A type 1-B/E 9606
124 5CPI 3 C, G Histone H2A type 1-B/E 9606
125 4JJN 3 C, G Histone H2A.2 4932
126 3W99 3 C, G Histone H2A type 1-B/E 9606
127 3AZE 3 C, G Histone H2A type 1-B/E 9606
128 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606
129 5CPJ 3 C, G Histone H2A type 1-B/E 9606
130 5B24 3 C, G Histone H2A type 1-B/E 9606
131 2HIO 1 A PROTEIN (HISTONE H2A) 9031
132 1HIO 1 A HISTONE H2A 9031
133 4QLC 5 C, G Histone H2A 7227
134 4LD9 3 C, G Histone H2A 8355
135 3O62 3 C, G Histone H2A type 1 8355
136 4XUJ 3 C, G Histone H2A UNP residues 2-126 8355
137 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227
138 3W97 3 C, G Histone H2A type 1-B/E 9606
139 4YM5 3 C, G Histone H2A type 1-B/E 9606
140 4YM6 3 C, G Histone H2A type 1-B/E 9606
141 2FJ7 5 C, G histone H2A 8355
142 3W98 3 C, G Histone H2A type 1-B/E 9606
143 4ZUX 3 C, G, M, Q Histone H2A type 1 8355
144 3AN2 3 C, G Histone H2A type 1-B/E 9606
145 3B6F 5 C, G Histone H2A 8355
146 5OY7 4 C, G, K, O, S, W, a, e Histone H2A 8355
147 3B6G 5 C, G Histone H2A 8355
148 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
149 3KXB 3 C, G Histone H2A 8355
150 3KWQ 3 C, G Histone H2A UNP residues 15-121 8355
151 5G2E 2 C, G, K, O, S, W HISTONE H2A TYPE 1 8355
152 5HQ2 3 G Histone H2A 8355
153 5OXV 3 C, G, M, Q Histone H2A 8355
154 1ZBB 5 C, G, c, g Histone H2A.1 8355
155 5O9G 3 C, G Histone H2A 8355
156 5X0X 3 C, G Histone H2A 8355
157 5X0Y 3 C, G Histone H2A 8355
158 5KGF 3 C, G Histone H2A type 1 Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin 9606
159 2RVQ 1 C Histone H2A type 1-B/E 9606
160 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031
161 3C9K 1 A, E Histone H2A-IV 9031