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 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 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355
43 3MVD 3 C, G Histone H2A 8355
44 4J8U 3 C, G Histone H2A type 1 8355
45 4WU9 3 C, G Histone H2A type 1 8355
46 3REH 3 C, G Histone H2A type 1 8355
47 3AZL 3 C, G Histone H2A type 1-B/E 9606
48 4XZQ 3 C, G Histone H2A residues 15-121 8355
49 3AFA 3 C, G Histone H2A type 1-B/E 9606
50 5E5A 4 C, G Histone H2A 8355
51 3REJ 3 C, G Histone H2A type 1 8355
52 3AZF 3 C, G Histone H2A type 1-B/E 9606
53 5GTC 3 C, G Histone H2A type 1-B/E 9606
54 1P3P 4 C, G Histone H2A 8355
55 3AV1 3 C, G Histone H2A type 1-B/E 9606
56 1M1A 4 C, G Histone H2A.1 8355
57 5CPK 3 C, G Histone H2A type 1-B/E 9606
58 5AY8 3 C, G Histone H2A type 1-B/E 9606
59 3MNN 3 C, G Histone H2A 8355
60 1P3G 4 C, G Histone H2A 8355
61 4J8W 3 C, G Histone H2A 8355
62 1P34 4 C, G Histone H2A 8355
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 2F8N 7 K Histone H2A type 1 10090
93 4Z5T 3 C, G Histone H2A type 1-B/E 9606
94 3AV2 3 C, G Histone H2A type 1-B/E 9606
95 3AYW 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 3REL 3 C, G Histone H2A 8355
102 5GSE 3 C, G, M Histone H2A type 1-B/E 9606
103 3REI 3 C, G Histone H2A type1 8355
104 1P3B 4 C, G Histone H2A 8355
105 3WKJ 3 C, G Histone H2A type 1-B/E 9606
106 4KUD 3 C, G Histone H2A.2 4932
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 1ID3 4 C, G HISTONE H2A.1 4932
117 3C1C 3 C, G Histone H2A type 1 8355
118 3AZH 3 C, G Histone H2A type 1-B/E 9606
119 5B40 3 C, G Histone H2A type 1-B/E 9606
120 5CPI 3 C, G Histone H2A type 1-B/E 9606
121 4JJN 3 C, G Histone H2A.2 4932
122 3W99 3 C, G Histone H2A type 1-B/E 9606
123 3AZE 3 C, G Histone H2A type 1-B/E 9606
124 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606
125 5CPJ 3 C, G Histone H2A type 1-B/E 9606
126 5B24 3 C, G Histone H2A type 1-B/E 9606
127 2HIO 1 A PROTEIN (HISTONE H2A) 9031
128 1HIO 1 A HISTONE H2A 9031
129 4QLC 5 C, G Histone H2A 7227
130 4LD9 3 C, G Histone H2A 8355
131 3O62 3 C, G Histone H2A type 1 8355
132 4XUJ 3 C, G Histone H2A UNP residues 2-126 8355
133 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227
134 3W97 3 C, G Histone H2A type 1-B/E 9606
135 4YM5 3 C, G Histone H2A type 1-B/E 9606
136 4YM6 3 C, G Histone H2A type 1-B/E 9606
137 2FJ7 5 C, G histone H2A 8355
138 3W98 3 C, G Histone H2A type 1-B/E 9606
139 4ZUX 3 C, G, M, Q Histone H2A type 1 8355
140 3AN2 3 C, G Histone H2A type 1-B/E 9606
141 3B6F 5 C, G Histone H2A 8355
142 3B6G 5 C, G Histone H2A 8355
143 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
144 3KXB 3 C, G Histone H2A 8355
145 3KWQ 3 C, G Histone H2A UNP residues 15-121 8355
146 5G2E 2 C, G, K, O, S, W HISTONE H2A TYPE 1 8355
147 5HQ2 3 G Histone H2A 8355
148 1ZBB 5 C, G, c, g Histone H2A.1 8355
149 5X0X 3 C, G Histone H2A 8355
150 5X0Y 3 C, G Histone H2A 8355
151 5KGF 3 C, G Histone H2A type 1 Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin 9606
152 2RVQ 1 C Histone H2A type 1-B/E 9606
153 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031
154 3C9K 1 A, E Histone H2A-IV 9031