Sequence Similarity Clusters for the Entities in PDB 1HQ3

Entity #1 | Chains: A,E
HISTONE H2A-IV protein, length: 129 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 6 6954
95 % 12 177 73 Flexibility: Low
Max RMSD: 6.8, Avg RMSD: 0.5
PDBFlex
90 % 12 186 74
70 % 13 194 85
50 % 14 205 107
40 % 14 205 127
30 % 14 205 139
Entity #2 | Chains: B,F
HISTONE H2B protein, length: 126 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 3 22 952
95 % 12 171 77 Flexibility: No
Max RMSD: 9.7, Avg RMSD: 0.5
PDBFlex
90 % 12 171 82
70 % 12 185 92
50 % 12 185 126
40 % 12 185 145
30 % 12 185 160
Entity #3 | Chains: C,G
HISTONE H3 protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 70 202
95 % 17 181 72 Flexibility: Low
Max RMSD: 11.4, Avg RMSD: 1.1
PDBFlex
90 % 17 188 76
70 % 17 189 88
50 % 17 193 118
40 % 17 193 142
30 % 17 193 153
Entity #4 | Chains: D,H
HISTONE H4-VI protein, length: 103 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 17 192 53
95 % 17 195 66 Flexibility: Low
Max RMSD: 13.3, Avg RMSD: 1.2
PDBFlex
90 % 17 203 69
70 % 17 203 83
50 % 17 203 111
40 % 17 203 132
30 % 17 203 144

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.

You can also use the structure comparison tool to compare any 2 given structures


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 3.2.1.21 | Details
7 5Y0D 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
8 5Y0C 4 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
9 1S32 4 C, G histone H2A 8355
10 5AV8 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
11 1KX3 4 C, G histone H2A.1 8355
12 5AV9 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
13 5AV6 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
14 1HQ3 1 A, E HISTONE H2A-IV 9031
15 3UTA 3 C, G Histone H2A 8355
16 4KHA 2 B Histone H2A UNP residues 15-103 8355
17 5X7X 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
18 5B31 3 C Histone H2A type 1-B/E 9606 3.2.1.21 | Details
19 5B31 5 G Histone H2A.Z 9606
20 5B1L 3 C, G Histone H2A type 1 10090
21 3UTB 3 C, G Histone H2A 8355
22 1M19 4 C, G Histone H2A.1 8355
23 5AVB 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
24 5AVC 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
25 5AV5 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
26 3C1B 3 C, G Histone H2A type 1 8355
27 5B1M 3 C, G Histone H2A type 1 10090
28 2NQB 4 C, G Histone H2A 7227
29 5OMX 5 C, G Histone H2A 8355
30 5F99 3 C, G Histone H2A type 1 8355
31 5Z30 3 C, G Histone H2A.Z 9606
32 5JRG 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
33 3UT9 3 C, G Histone H2A 8355
34 5B32 3 C Histone H2A type 1-B/E 9606 3.2.1.21 | Details
35 5B32 5 G Histone H2A.Z 9606
36 4WU8 5 C, G Histone H2A type 1 8355
37 1P3I 4 C, G Histone H2A 8355
38 3MGR 3 C, G Histone H2A UNP RESIDUES 2-120 8355
39 1F66 4 C, G HISTONE H2A.Z 9606
40 3AZG 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
41 5FUG 1 A, D, G, J HISTONE H2A.Z GLOBULAR DOMAIN 9606
42 1M18 4 C, G Histone H2A.1 8355
43 5B2J 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
44 2PYO 5 C, G Histone H2A 7227
45 1P3L 4 C, G Histone H2A 8355
46 1EQZ 2 A, E PROTEIN (HISTONE H2A) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031
47 5B0Y 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
48 2CV5 4 C, G Histone H2A.a 9606 3.2.1.21 | Details
49 5CP6 5 C, G Histone H2A 8355
50 5BT1 2 C Histone H2A.1 4932
51 5XF6 3 C, G Histone H2A 8355
52 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355
53 3MVD 3 C, G Histone H2A 8355
54 4J8U 3 C, G Histone H2A type 1 8355
55 4WU9 3 C, G Histone H2A type 1 8355
56 3REH 3 C, G Histone H2A type 1 8355
57 3AZL 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
58 4XZQ 3 C, G Histone H2A residues 15-121 8355
59 3AFA 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
60 5E5A 4 C, G Histone H2A 8355
61 3REJ 3 C, G Histone H2A type 1 8355
62 3AZF 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
63 5GTC 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
64 1P3P 4 C, G Histone H2A 8355
65 3AV1 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
66 1M1A 4 C, G Histone H2A.1 8355
67 5CPK 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
68 5AY8 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
69 3MNN 3 C, G Histone H2A 8355
70 1P3G 4 C, G Histone H2A 8355
71 4J8W 3 C, G Histone H2A 8355
72 1P34 4 C, G Histone H2A 8355
73 5XF3 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
74 3X1V 4 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
75 5MLU 3 C, G Histone H2A type 1 8355
76 5ONG 5 C, G Histone H2A 8355
77 5ONW 5 C, G Histone H2A 8355
78 5DNM 3 C, G Histone H2A 8355
79 4Z66 3 C, G Histone H2A 8355
80 3MGQ 3 C, G Histone H2A UNP RESIDUES 2-120 8355
81 3WTP 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
82 3X1T 4 C, G Histone H2A 10090
83 2NZD 5 C, G histone H2A 8355
84 3A6N 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
85 5DNN 3 C, G Histone H2A 8355
86 5GT3 3 C, G Histone H2A type 1-D 9606
87 5GT0 3 C, G Histone H2A type 1-A 9606
88 3LJA 3 C, G Histone H2A 8355
89 3AZI 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
90 3TU4 3 C, G Histone H2A 8355
91 1P3O 4 C, G Histone H2A 8355
92 1KX4 4 C, G histone H2A.1 8355
93 3AZN 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
94 1P3M 4 C, G Histone H2A 8355
95 4J8V 3 C, G Histone H2A 8355
96 5B33 3 C, G Histone H2A.Z 9606
97 1AOI 4 C, G HISTONE H2A HISTONE H2A 8355
98 3X1S 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
99 3LZ0 3 C, G Histone H2A residues 2-120 8355
100 1P3F 4 C, G Histone H2A 8355
101 1P3K 4 C, G Histone H2A 8355
102 5B2I 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
103 1P3A 4 C, G Histone H2A 8355
104 3LZ1 3 C, G Histone H2A residues 2-120 8355
105 5GXQ 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
106 2F8N 6 G Core histone macro-H2A.1 residues 0-119 9606
107 2F8N 7 K Histone H2A type 1 10090
108 4Z5T 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
109 1U35 4 C, G H2A histone family 9606
110 5XM0 3 C, G Histone H2A type 1-B 10090
111 3AV2 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
112 3AYW 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
113 5XF5 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
114 3AZJ 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
115 3REK 3 C, G Histone H2A type1 8355
116 4KGC 3 C, G Histone H2A 8355
117 1ZLA 4 C, G Xenopus laevis-like histone H2A 263730
118 5GSU 3 C, G Histone H2A type 1-A 9606
119 5XF4 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
120 3REL 3 C, G Histone H2A 8355
121 5GSE 3 C, G, M Histone H2A type 1-B/E 9606 3.2.1.21 | Details
122 3REI 3 C, G Histone H2A type1 8355
123 1P3B 4 C, G Histone H2A 8355
124 3WKJ 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
125 4KUD 3 C, G Histone H2A.2 4932
126 3AZK 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
127 4J8X 3 C, G Histone H2A 8355
128 3LEL 3 C, G, M, Q Histone H2A 8355
129 4YS3 3 C, G Histone H2A residues 15-121 8355
130 3KUY 3 C, G Histone H2A 8355
131 4R8P 3 C, G Histone H2A 8355
132 3AZM 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
133 3X1U 4 C, G Histone H2A 10090
134 3MGS 3 C, G Histone H2A UNP RESIDUES 2-120 8355
135 3WA9 3 C, G Histone H2A.Z 9606
136 1ID3 4 C, G HISTONE H2A.1 4932
137 3C1C 3 C, G Histone H2A type 1 8355
138 3AZH 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
139 5B40 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
140 3WAA 3 C, G Histone H2A.V 9606
141 5CPI 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
142 4JJN 3 C, G Histone H2A.2 4932
143 3W99 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
144 3AZE 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
145 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606 3.2.1.21 | Details
146 5XM1 3 C, G Histone H2A type 1-B 10090
147 5CPJ 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
148 5B24 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
149 2HIO 1 A PROTEIN (HISTONE H2A) 9031
150 1HIO 1 A HISTONE H2A 9031
151 4QLC 5 C, G Histone H2A 7227
152 4LD9 3 C, G Histone H2A 8355
153 3O62 3 C, G Histone H2A type 1 8355
154 4XUJ 3 C, G Histone H2A UNP residues 2-126 8355
155 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227
156 3W97 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
157 4YM5 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
158 4YM6 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
159 2FJ7 5 C, G histone H2A 8355
160 3W98 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
161 4ZUX 3 C, G, M, Q Histone H2A type 1 8355
162 3AN2 3 C, G Histone H2A type 1-B/E 9606 3.2.1.21 | Details
163 5WCU 3 C, G, M, Q Histone H2A UNP residues 15-118 7227
164 3B6F 5 C, G Histone H2A 8355
165 5OY7 4 C, G, K, O, S, W, a, e Histone H2A 8355
166 3B6G 5 C, G Histone H2A 8355
167 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
168 3KXB 3 C, G Histone H2A 8355
169 3KWQ 3 C, G Histone H2A UNP residues 15-121 8355
170 5G2E 2 C, G, K, O, S, W HISTONE H2A TYPE 1 8355
171 5HQ2 3 G Histone H2A 8355
172 6HKT 3 0, 2, C, G, M, Q, W, c, g, m, q, w Histone H2A type 1-B/E THE 3 N-TERMINAL RESIDUES (GSH) COME FROM THE EXPRESSION TAG 9606 3.2.1.21 | Details
173 5OXV 3 C, G, M, Q Histone H2A 8355
174 1ZBB 5 C, G, c, g Histone H2A.1 8355
175 6I84 2 Q, V Histone H2A type 1 8355
176 6HTS 7 K, O Histone H2A type 1-B/E 9606 3.2.1.21 | Details
177 6A5O 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
178 6A5P 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
179 6A5R 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
180 6A5T 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
181 6A5U 18 c, g Histone H2A, Histone H2A type 1-B/E 9606 3.2.1.21 | Details
182 6A5V 18 c, g Histone H2A, Histone H2A type 1-B/E 9606 3.2.1.21 | Details
183 6A5L 18 c, g Histone H2A type 1-B/E 9606 3.2.1.21 | Details
184 6GEN 4 E, F Histone H2A.1 4932
185 6GEJ 4 E, F Histone H2A.1 4932
186 6G0L 3 C Histone H2A type 1 8355
187 6G0L 5 G Histone H2A type 1 8355
188 6FTX 3 C, G Histone H2A type 1 8355
189 6FQ5 3 C, G Histone H2A 8355
190 6FQ6 3 C, G Histone H2A 8355
191 6FQ8 3 C, G Histone H2A 8355
192 6FML 11 O, S Histone H2A type 1 9606
193 6C0W 3 C, G Histone H2A 9606
194 6BUZ 3 C, G Histone H2A 9606 3.2.1.21 | Details
195 6ESF 3 C, G Histone H2A 8355
196 6ESG 3 C, G Histone H2A 8355
197 6ESH 3 C, G Histone H2A 8355
198 6ESI 3 C, G Histone H2A 8355
199 5O9G 3 C, G Histone H2A 8355
200 5X0X 3 C, G Histone H2A 8355
201 5X0Y 3 C, G Histone H2A 8355
202 5KGF 3 C, G Histone H2A type 1 Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin 9606
203 2RVQ 1 C Histone H2A type 1-B/E 9606 3.2.1.21 | Details
204 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031
205 3C9K 1 A, E Histone H2A-IV 9031