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 42 304
95 % 52 150 76 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.3
PDBFlex
90 % 52 153 77
70 % 52 154 96
50 % 53 157 131
40 % 53 157 146
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 74 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 57 165 75
70 % 57 165 87
50 % 57 165 123
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 54 245
95 % 45 140 86 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.5
PDBFlex
90 % 47 148 78
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 48 265
95 % 44 135 111 Flexibility: Low
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 44 140 107
70 % 47 147 104
50 % 47 147 140
40 % 47 147 156
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 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 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355
48 3MVD 3 C, G Histone H2A 8355
49 4J8U 3 C, G Histone H2A type 1 8355
50 4WU9 3 C, G Histone H2A type 1 8355
51 3REH 3 C, G Histone H2A type 1 8355
52 3AZL 3 C, G Histone H2A type 1-B/E 9606
53 4XZQ 3 C, G Histone H2A residues 15-121 8355
54 3AFA 3 C, G Histone H2A type 1-B/E 9606
55 5E5A 4 C, G Histone H2A 8355
56 3REJ 3 C, G Histone H2A type 1 8355
57 3AZF 3 C, G Histone H2A type 1-B/E 9606
58 5GTC 3 C, G Histone H2A type 1-B/E 9606
59 1P3P 4 C, G Histone H2A 8355
60 3AV1 3 C, G Histone H2A type 1-B/E 9606
61 1M1A 4 C, G Histone H2A.1 8355
62 5CPK 3 C, G Histone H2A type 1-B/E 9606
63 5AY8 3 C, G Histone H2A type 1-B/E 9606
64 3MNN 3 C, G Histone H2A 8355
65 1P3G 4 C, G Histone H2A 8355
66 4J8W 3 C, G Histone H2A 8355
67 1P34 4 C, G Histone H2A 8355
68 3X1V 4 C, G Histone H2A type 1-B/E 9606
69 5MLU 3 C, G Histone H2A type 1 8355
70 5DNM 3 C, G Histone H2A 8355
71 4Z66 3 C, G Histone H2A 8355
72 3MGQ 3 C, G Histone H2A UNP RESIDUES 2-120 8355
73 3WTP 3 C, G Histone H2A type 1-B/E 9606
74 3X1T 4 C, G Histone H2A 10090
75 2NZD 5 C, G histone H2A 8355
76 3A6N 3 C, G Histone H2A type 1-B/E 9606
77 5DNN 3 C, G Histone H2A 8355
78 5GT3 3 C, G Histone H2A type 1-D 9606
79 5GT0 3 C, G Histone H2A type 1-A 9606
80 3LJA 3 C, G Histone H2A 8355
81 3AZI 3 C, G Histone H2A type 1-B/E 9606
82 3TU4 3 C, G Histone H2A 8355
83 1P3O 4 C, G Histone H2A 8355
84 1KX4 4 C, G histone H2A.1 8355
85 3AZN 3 C, G Histone H2A type 1-B/E 9606
86 1P3M 4 C, G Histone H2A 8355
87 4J8V 3 C, G Histone H2A 8355
88 5B33 3 C, G Histone H2A.Z 9606
89 1AOI 4 C, G HISTONE H2A HISTONE H2A 8355
90 3X1S 3 C, G Histone H2A type 1-B/E 9606
91 3LZ0 3 C, G Histone H2A residues 2-120 8355
92 1P3F 4 C, G Histone H2A 8355
93 1P3K 4 C, G Histone H2A 8355
94 5B2I 3 C, G Histone H2A type 1-B/E 9606
95 1P3A 4 C, G Histone H2A 8355
96 3LZ1 3 C, G Histone H2A residues 2-120 8355
97 5GXQ 3 C, G Histone H2A type 1-B/E 9606
98 2F8N 6 G Core histone macro-H2A.1 residues 0-119 9606
99 2F8N 7 K Histone H2A type 1 10090
100 4Z5T 3 C, G Histone H2A type 1-B/E 9606
101 1U35 4 C, G H2A histone family 9606
102 3AV2 3 C, G Histone H2A type 1-B/E 9606
103 3AYW 3 C, G Histone H2A type 1-B/E 9606
104 3AZJ 3 C, G Histone H2A type 1-B/E 9606
105 3REK 3 C, G Histone H2A type1 8355
106 4KGC 3 C, G Histone H2A 8355
107 1ZLA 4 C, G Xenopus laevis-like histone H2A 263730
108 5GSU 3 C, G Histone H2A type 1-A 9606
109 3REL 3 C, G Histone H2A 8355
110 5GSE 3 C, G, M Histone H2A type 1-B/E 9606
111 3REI 3 C, G Histone H2A type1 8355
112 1P3B 4 C, G Histone H2A 8355
113 3WKJ 3 C, G Histone H2A type 1-B/E 9606
114 4KUD 3 C, G Histone H2A.2 4932
115 3AZK 3 C, G Histone H2A type 1-B/E 9606
116 4J8X 3 C, G Histone H2A 8355
117 3LEL 3 C, G, M, Q Histone H2A 8355
118 4YS3 3 C, G Histone H2A residues 15-121 8355
119 3KUY 3 C, G Histone H2A 8355
120 4R8P 3 C, G Histone H2A 8355
121 3AZM 3 C, G Histone H2A type 1-B/E 9606
122 3X1U 4 C, G Histone H2A 10090
123 3MGS 3 C, G Histone H2A UNP RESIDUES 2-120 8355
124 3WA9 3 C, G Histone H2A.Z 9606
125 1ID3 4 C, G HISTONE H2A.1 4932
126 3C1C 3 C, G Histone H2A type 1 8355
127 3AZH 3 C, G Histone H2A type 1-B/E 9606
128 5B40 3 C, G Histone H2A type 1-B/E 9606
129 3WAA 3 C, G Histone H2A.V 9606
130 5CPI 3 C, G Histone H2A type 1-B/E 9606
131 4JJN 3 C, G Histone H2A.2 4932
132 3W99 3 C, G Histone H2A type 1-B/E 9606
133 3AZE 3 C, G Histone H2A type 1-B/E 9606
134 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606
135 5CPJ 3 C, G Histone H2A type 1-B/E 9606
136 5B24 3 C, G Histone H2A type 1-B/E 9606
137 2HIO 1 A PROTEIN (HISTONE H2A) 9031
138 1HIO 1 A HISTONE H2A 9031
139 4QLC 5 C, G Histone H2A 7227
140 4LD9 3 C, G Histone H2A 8355
141 3O62 3 C, G Histone H2A type 1 8355
142 4XUJ 3 C, G Histone H2A UNP residues 2-126 8355
143 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227
144 3W97 3 C, G Histone H2A type 1-B/E 9606
145 4YM5 3 C, G Histone H2A type 1-B/E 9606
146 4YM6 3 C, G Histone H2A type 1-B/E 9606
147 2FJ7 5 C, G histone H2A 8355
148 3W98 3 C, G Histone H2A type 1-B/E 9606
149 4ZUX 3 C, G, M, Q Histone H2A type 1 8355
150 3AN2 3 C, G Histone H2A type 1-B/E 9606
151 3B6F 5 C, G Histone H2A 8355
152 3B6G 5 C, G Histone H2A 8355
153 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
154 3KXB 3 C, G Histone H2A 8355
155 3KWQ 3 C, G Histone H2A UNP residues 15-121 8355
156 5G2E 2 C, G, K, O, S, W HISTONE H2A TYPE 1 8355
157 5HQ2 3 G Histone H2A 8355
158 1ZBB 5 C, G, c, g Histone H2A.1 8355
159 5X0X 3 C, G Histone H2A 8355
160 5X0Y 3 C, G Histone H2A 8355
161 5KGF 3 C, G Histone H2A type 1 Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin 9606
162 2RVQ 1 C Histone H2A type 1-B/E 9606
163 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031
164 3C9K 1 A, E Histone H2A-IV 9031