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