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 42 306
95 % 52 150 77 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.2
PDBFlex
90 % 52 153 78
70 % 52 154 96
50 % 53 157 132
40 % 53 157 147
30 % 53 157 161
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 % 51 141 76
95 % 56 160 75 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 57 165 75
70 % 57 165 86
50 % 57 165 124
40 % 57 165 140
30 % 57 165 155
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 54 247
95 % 45 140 86 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.5
PDBFlex
90 % 47 148 79
70 % 49 154 90
50 % 54 164 120
40 % 54 164 139
30 % 54 164 152
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 48 267
95 % 44 135 111 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 44 140 107
70 % 47 147 103
50 % 47 147 140
40 % 47 147 157
30 % 47 147 174
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 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355
41 3MVD 3 C, G Histone H2A 8355
42 4J8U 3 C, G Histone H2A type 1 8355
43 4WU9 3 C, G Histone H2A type 1 8355
44 3REH 3 C, G Histone H2A type 1 8355
45 3AZL 3 C, G Histone H2A type 1-B/E 9606
46 4XZQ 3 C, G Histone H2A residues 15-121 8355
47 3AFA 3 C, G Histone H2A type 1-B/E 9606
48 5E5A 4 C, G Histone H2A 8355
49 3REJ 3 C, G Histone H2A type 1 8355
50 3AZF 3 C, G Histone H2A type 1-B/E 9606
51 5GTC 3 C, G Histone H2A type 1-B/E 9606
52 1P3P 4 C, G Histone H2A 8355
53 3AV1 3 C, G Histone H2A type 1-B/E 9606
54 1M1A 4 C, G Histone H2A.1 8355
55 5CPK 3 C, G Histone H2A type 1-B/E 9606
56 5AY8 3 C, G Histone H2A type 1-B/E 9606
57 3MNN 3 C, G Histone H2A 8355
58 1P3G 4 C, G Histone H2A 8355
59 4J8W 3 C, G Histone H2A 8355
60 1P34 4 C, G Histone H2A 8355
61 3X1V 4 C, G Histone H2A type 1-B/E 9606
62 5MLU 3 C, G Histone H2A type 1 8355
63 5DNM 3 C, G Histone H2A 8355
64 4Z66 3 C, G Histone H2A 8355
65 3MGQ 3 C, G Histone H2A UNP RESIDUES 2-120 8355
66 3WTP 3 C, G Histone H2A type 1-B/E 9606
67 3X1T 4 C, G Histone H2A 10090
68 2NZD 5 C, G histone H2A 8355
69 3A6N 3 C, G Histone H2A type 1-B/E 9606
70 5DNN 3 C, G Histone H2A 8355
71 5GT3 3 C, G Histone H2A type 1-D 9606
72 5GT0 3 C, G Histone H2A type 1-A 9606
73 3LJA 3 C, G Histone H2A 8355
74 3AZI 3 C, G Histone H2A type 1-B/E 9606
75 3TU4 3 C, G Histone H2A 8355
76 1P3O 4 C, G Histone H2A 8355
77 1KX4 4 C, G histone H2A.1 8355
78 3AZN 3 C, G Histone H2A type 1-B/E 9606
79 1P3M 4 C, G Histone H2A 8355
80 4J8V 3 C, G Histone H2A 8355
81 1AOI 4 C, G HISTONE H2A HISTONE H2A 8355
82 3X1S 3 C, G Histone H2A type 1-B/E 9606
83 3LZ0 3 C, G Histone H2A residues 2-120 8355
84 1P3F 4 C, G Histone H2A 8355
85 1P3K 4 C, G Histone H2A 8355
86 5B2I 3 C, G Histone H2A type 1-B/E 9606
87 1P3A 4 C, G Histone H2A 8355
88 3LZ1 3 C, G Histone H2A residues 2-120 8355
89 5GXQ 3 C, G Histone H2A type 1-B/E 9606
90 4Z5T 3 C, G Histone H2A type 1-B/E 9606
91 3AV2 3 C, G Histone H2A type 1-B/E 9606
92 3AYW 3 C, G Histone H2A type 1-B/E 9606
93 3AZJ 3 C, G Histone H2A type 1-B/E 9606
94 3REK 3 C, G Histone H2A type1 8355
95 4KGC 3 C, G Histone H2A 8355
96 1ZLA 4 C, G Xenopus laevis-like histone H2A 263730
97 5GSU 3 C, G Histone H2A type 1-A 9606
98 3REL 3 C, G Histone H2A 8355
99 5GSE 3 C, G, M Histone H2A type 1-B/E 9606
100 3REI 3 C, G Histone H2A type1 8355
101 1P3B 4 C, G Histone H2A 8355
102 3WKJ 3 C, G Histone H2A type 1-B/E 9606
103 3AZK 3 C, G Histone H2A type 1-B/E 9606
104 4J8X 3 C, G Histone H2A 8355
105 3LEL 3 C, G, M, Q Histone H2A 8355
106 4YS3 3 C, G Histone H2A residues 15-121 8355
107 3KUY 3 C, G Histone H2A 8355
108 4R8P 3 C, G Histone H2A 8355
109 3AZM 3 C, G Histone H2A type 1-B/E 9606
110 3X1U 4 C, G Histone H2A 10090
111 3MGS 3 C, G Histone H2A UNP RESIDUES 2-120 8355
112 3C1C 3 C, G Histone H2A type 1 8355
113 3AZH 3 C, G Histone H2A type 1-B/E 9606
114 5B40 3 C, G Histone H2A type 1-B/E 9606
115 5CPI 3 C, G Histone H2A type 1-B/E 9606
116 3W99 3 C, G Histone H2A type 1-B/E 9606
117 3AZE 3 C, G Histone H2A type 1-B/E 9606
118 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606
119 5CPJ 3 C, G Histone H2A type 1-B/E 9606
120 5B24 3 C, G Histone H2A type 1-B/E 9606
121 2HIO 1 A PROTEIN (HISTONE H2A) 9031
122 1HIO 1 A HISTONE H2A 9031
123 4QLC 5 C, G Histone H2A 7227
124 4LD9 3 C, G Histone H2A 8355
125 3O62 3 C, G Histone H2A type 1 8355
126 4XUJ 3 C, G Histone H2A UNP residues 2-126 8355
127 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227
128 3W97 3 C, G Histone H2A type 1-B/E 9606
129 4YM5 3 C, G Histone H2A type 1-B/E 9606
130 4YM6 3 C, G Histone H2A type 1-B/E 9606
131 2FJ7 5 C, G histone H2A 8355
132 3W98 3 C, G Histone H2A type 1-B/E 9606
133 4ZUX 3 C, G, M, Q Histone H2A type 1 8355
134 3AN2 3 C, G Histone H2A type 1-B/E 9606
135 3B6F 5 C, G Histone H2A 8355
136 3B6G 5 C, G Histone H2A 8355
137 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
138 3KXB 3 C, G Histone H2A 8355
139 3KWQ 3 C, G Histone H2A UNP residues 15-121 8355
140 5G2E 2 C, G, K, O, S, W HISTONE H2A TYPE 1 8355
141 5HQ2 3 G Histone H2A 8355
142 1ZBB 5 C, G, c, g Histone H2A.1 8355
143 5X0X 3 C, G Histone H2A 8355
144 5X0Y 3 C, G Histone H2A 8355
145 5KGF 3 C, G Histone H2A type 1 Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin 9606
146 2RVQ 1 C Histone H2A type 1-B/E 9606
147 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031
148 3C9K 1 A, E Histone H2A-IV 9031