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The human nucleosome structure
Sequence Clustering and Redundancy Reduction Results
3AFA
Cluster # 163 Members. Sequence cutoff: 50% Cluster size: 108 sequences
Rank   PDB id Entity id Chains Description Details Taxonomy EC Number
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1 1TZY 3 C, G HISTONE H3 9031  
2 4H9N 1 A Histone H3.3 9606  
3 4H9Q 1 A Histone H3.3 9606  
4 1KX5 3 A, E histone H3 8355  
5 4H9O 1 A Histone H3.3 9606  
6 2ARO 3 C, G HISTONE H3 9031  
7 4H9R 1 A Histone H3.3 9606  
8 1S32 2 A, E histone H3 8355  
9 4H9P 1 A Histone H3.3 9606  
10 1KX3 2 A, E histone H3 8355  
11 1HQ3 3 C, G HISTONE H3 9031  
12 3UTA 1 A, E Histone H3.2 8355  
13 3UTB 1 A, E Histone H3.2 8355  
14 1M19 2 A, E Histone H3.2 8355  
15 3C1B 1 A, E Histone H3-like 8355  
16 2NQB 2 A, E Histone H3 7227  
17 3UT9 1 A, E Histone H3.2 8355  
18 4WU8 3 A, E Histone H3.2 8355  
19 1P3I 2 A, E Histone H3 8355  
20 3MGR 1 A, E Histone H3.2 8355  
21 1F66 2 A, E HISTONE H3 8355  
22 3AZG 1 A, E Histone H3.1 9606  
23 4H9S 1 A, B Histone H3.3 9606  
24 1M18 2 A, E Histone H3.2 8355  
25 2PYO 3 A, E Histone H3 7227  
26 1P3L 2 A, E Histone H3 8355  
27 1EQZ 4 C, G PROTEIN (HISTONE H3) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031  
28 2CV5 2 A, E Histone H3.1 9606  
29 3MGP 1 A, E Histone H3.2 8355  
30 3MVD 1 A, E Histone H3.2 8355  
31 4J8U 1 A, E Histone H3.2 8355  
32 4WU9 1 A, E Histone H3.2 8355  
33 3REH 1 A, E Histone H3.2 8355  
34 3AZL 1 A, E Histone H3.1 9606  
35 3NQU 1 A Histone H3-like centromeric protein A 9606  
36 3AFA 1 A, E Histone H3.1 9606  
37 3REJ 1 A, E Histone H3.2 8355  
38 3AZF 1 A, E Histone H3.1 9606  
39 1P3P 2 A, E Histone H3 8355  
40 3AV1 1 A, E Histone H3.2 9606  
41 1M1A 2 A, E Histone H3.2 8355  
42 3MNN 1 A, E Histone H3.2 8355  
43 1P3G 2 A, E Histone H3 8355  
44 4J8W 1 A, E Histone H3.2 8355  
45 1P34 2 A, E Histone H3 8355  
46 4HGA 2 B Histone H3.3 9606  
47 4UUZ 1 A HISTONE H3 7227  
48 3MGQ 1 A, E Histone H3.2 8355  
49 3WTP 1 A Histone H3-like centromeric protein A 9606  
50 3WTP 5 E Histone H3.3 9606  
51 2NZD 3 A, E Histone H3 8355  
52 3A6N 1 A, E Histone H3.1t 9606  
53 3LJA 1 A, E Histone H3.2 8355  
54 3AZI 1 A, E Histone H3.1 9606  
55 3TU4 1 A, E Histone H3.2 8355  
56 1P3O 2 A, E Histone H3 8355  
57 1KX4 2 A, E histone H3 8355  
58 3AZN 1 A, E Histone H3.1 9606  
59 1P3M 2 A, E Histone H3 8355  
60 4J8V 1 A, E Histone H3.2 8355  
61 3LZ0 1 A, E Histone H3.2 8355  
62 1P3F 2 A, E Histone H3 8355  
63 1P3K 2 A, E Histone H3 8355  
64 1P3A 2 A, E Histone H3 8355  
65 3LZ1 1 A, E Histone H3.2 8355  
66 2IO5 2 B Histone H3.1 8355  
67 2F8N 2 A, E Histone H3.1 8355  
68 1U35 2 A, E Histone H3.1 10090  
69 3AV2 1 A, E Histone H3.3 9606  
70 3AYW 1 A, E Histone H3.1 9606  
71 3AZJ 1 A, E Histone H3.1 9606  
72 3REK 1 A, E Histone H3.2 8355  
73 4KGC 1 A, E Histone H3.2 8355  
74 1ZLA 2 A, E histone H3 8355  
75 3REL 1 A, E Histone H3.2 8355  
76 3REI 1 A, E Histone H3.2 8355  
77 1P3B 2 A, E Histone H3 8355  
78 3WKJ 1 A, E Histone H3.1 9606  
79 4KUD 1 A, E Histone H3 559292  
80 3AZK 1 A, E Histone H3.1 9606  
81 4J8X 1 A, E Histone H3.2 8355  
82 3LEL 1 A, E, K, O Histone H3.2 8355  
83 3KUY 1 A, E Histone H3.2 8355  
84 4R8P 1 A, E Histone H3.2 8355  
85 3AZM 1 A, E Histone H3.1 9606  
86 3MGS 1 A, E Histone H3.2 8355  
87 3WA9 1 A, E Histone H3.1 9606  
88 1ID3 2 A, E HISTONE H3 4932  
89 3C1C 1 A, E Histone H3-like 8355  
90 3AZH 1 A, E Histone H3.1 9606  
91 3WAA 1 A, E Histone H3.1 9606  
92 4JJN 1 A, E Histone H3 559292  
93 3W99 1 A, E Histone H3.1 9606  
94 3AZE 1 A, E Histone H3.1 9606  
95 3W96 1 A, E Histone H3.1 9606  
96 5C3I 2 B, F, J, N, R, V Histone H3.1 9606  
97 2HIO 3 C PROTEIN (HISTONE H3) 9031  
98 4QLC 3 A, E Histone H3 7227  
99 4LD9 1 A, E Histone H3.2 8355  
100 3O62 1 A, E Histone H3.2 8355  
101 3W97 1 A, E Histone H3.1 9606  
102 2FJ7 3 A, E histone H3 8355  
103 3AN2 1 A, E Histone H3-like centromeric protein A 9606  
104 3B6F 3 A, E Histone H3.2 8355  
105 3B6G 3 A, E Histone H3.2 8355  
106 3KXB 1 A, E Histone H3.2 8355  
107 1ZBB 3 A, E, a, e HISTONE H3 8355  
108 3C9K 3 C, G Histone H3.2 9031  
 
Sequence Clusters for the Sequence Entities in PDB 3AFA
Entity #1: Chains: A,E - Histone H3.1 protein, length: 139 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 3 16 866
95% 35 102 121
90% 35 105 126
70% 35 105 141
50% 36 108 163
40% 36 108 183
30% 36 108 197
Entity #2: Chains: B,F - Histone H4 protein, length: 106 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 34 92 95
95% 38 109 113
90% 39 113 97
70% 39 113 117
50% 39 113 152
40% 39 113 169
30% 39 113 186
Entity #3: Chains: C,G - Histone H2A type 1-B/E protein, length: 133 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 4 23 623
95% 26 88 136
90% 29 95 132
70% 29 98 146
50% 31 104 164
40% 31 104 184
30% 31 104 198
Entity #4: Chains: D,H - Histone H2B type 1-J protein, length: 129 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 3 22 687
95% 27 88 137
90% 27 90 146
70% 29 97 153
50% 29 97 182
40% 29 97 197
30% 29 97 215
Entity #5: Chains: I,J - 146-MER DNA dna, length: 146 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
 

Documentation

Click here for more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB.