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The human nucleosome structure
Sequence Clustering and Redundancy Reduction Results
3AFA
Cluster # 160 Members. Sequence cutoff: 40% Cluster size: 101 sequences
Rank   PDB id Entity id Chains Description Details Taxonomy EC Number
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1 4CAY 1 A HISTONE H2A.Z GLOBULAR DOMAIN, RESIDUES 19-128 9606  
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 1S32 4 C, G histone H2A 8355  
6 1KX3 4 C, G histone H2A.1 8355  
7 1HQ3 1 A, E HISTONE H2A-IV 9031  
8 3UTA 3 C, G Histone H2A 8355  
9 4KHA 2 B Histone H2A UNP residues 15-103 8355  
10 3UTB 3 C, G Histone H2A 8355  
11 1M19 4 C, G Histone H2A.1 8355  
12 3C1B 3 C, G Histone H2A type 1 8355  
13 2NQB 4 C, G Histone H2A 7227  
14 3UT9 3 C, G Histone H2A 8355  
15 1P3I 4 C, G Histone H2A 8355  
16 3MGR 3 C, G Histone H2A UNP RESIDUES 2-120 8355  
17 1F66 4 C, G HISTONE H2A.Z 9606  
18 3AZG 3 C, G Histone H2A type 1-B/E 9606  
19 1M18 4 C, G Histone H2A.1 8355  
20 2PYO 5 C, G Histone H2A 7227  
21 1P3L 4 C, G Histone H2A 8355  
22 1EQZ 2 A, E PROTEIN (HISTONE H2A) SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER 9031  
23 2CV5 4 C, G Histone H2A.a 9606  
24 3MGP 3 C, G Histone H2A UNP RESIDUES 2-120 8355  
25 3MVD 3 C, G Histone H2A 8355  
26 4J8U 3 C, G Histone H2A type 1 8355  
27 3REH 3 C, G Histone H2A type 1 8355  
28 3AZL 3 C, G Histone H2A type 1-B/E 9606  
29 3AFA 3 C, G Histone H2A type 1-B/E 9606  
30 3REJ 3 C, G Histone H2A type 1 8355  
31 3AZF 3 C, G Histone H2A type 1-B/E 9606  
32 1P3P 4 C, G Histone H2A 8355  
33 3AV1 3 C, G Histone H2A type 1-B/E 9606  
34 1M1A 4 C, G Histone H2A.1 8355  
35 3MNN 3 C, G Histone H2A 8355  
36 1P3G 4 C, G Histone H2A 8355  
37 4J8W 3 C, G Histone H2A 8355  
38 1P34 4 C, G Histone H2A 8355  
39 3MGQ 3 C, G Histone H2A UNP RESIDUES 2-120 8355  
40 3WTP 3 C, G Histone H2A type 1-B/E 9606  
41 2NZD 5 C, G histone H2A 8355  
42 3A6N 3 C, G Histone H2A type 1-B/E 9606  
43 3LJA 3 C, G Histone H2A 8355  
44 3AZI 3 C, G Histone H2A type 1-B/E 9606  
45 3TU4 3 C, G Histone H2A 8355  
46 1P3O 4 C, G Histone H2A 8355  
47 1KX4 4 C, G histone H2A.1 8355  
48 3AZN 3 C, G Histone H2A type 1-B/E 9606  
49 1P3M 4 C, G Histone H2A 8355  
50 4J8V 3 C, G Histone H2A 8355  
51 1AOI 4 C, G HISTONE H2A HISTONE H2A 8355  
52 3LZ0 3 C, G Histone H2A residues 2-120 8355  
53 1P3F 4 C, G Histone H2A 8355  
54 1P3K 4 C, G Histone H2A 8355  
55 1P3A 4 C, G Histone H2A 8355  
56 3LZ1 3 C, G Histone H2A residues 2-120 8355  
57 2F8N 6 G Core histone macro-H2A.1 residues 0-119 9606  
58 1U35 4 C, G H2A histone family 9606  
59 3AV2 3 C, G Histone H2A type 1-B/E 9606  
60 3AYW 3 C, G Histone H2A type 1-B/E 9606  
61 3AZJ 3 C, G Histone H2A type 1-B/E 9606  
62 3REK 3 C, G Histone H2A type1 8355  
63 4KGC 3 C, G Histone H2A 8355  
64 1ZLA 4 C, G Xenopus laevis-like histone H2A 263730  
65 3REL 3 C, G Histone H2A 8355  
66 3REI 3 C, G Histone H2A type1 8355  
67 1P3B 4 C, G Histone H2A 8355  
68 3WKJ 3 C, G Histone H2A type 1-B/E 9606  
69 4KUD 3 C, G Histone H2A.2 559292  
70 3AZK 3 C, G Histone H2A type 1-B/E 9606  
71 4J8X 3 C, G Histone H2A 8355  
72 3LEL 3 C, G, M, Q Histone H2A 8355  
73 3KUY 3 C, G Histone H2A 8355  
74 4R8P 3 C, G Histone H2A 8355  
75 3AZM 3 C, G Histone H2A type 1-B/E 9606  
76 3MGS 3 C, G Histone H2A UNP RESIDUES 2-120 8355  
77 3WA9 3 C, G Histone H2A.Z 9606  
78 1ID3 4 C, G HISTONE H2A.1 4932  
79 3C1C 3 C, G Histone H2A type 1 8355  
80 3AZH 3 C, G Histone H2A type 1-B/E 9606  
81 3WAA 3 C, G Histone H2A.V 9606  
82 4JJN 3 C, G Histone H2A.2 559292  
83 3W99 3 C, G Histone H2A type 1-B/E 9606  
84 3AZE 3 C, G Histone H2A type 1-B/E 9606  
85 3W96 3 C, G Histone H2A type 1-B/E UNP residues 11-130 9606  
86 2HIO 1 A PROTEIN (HISTONE H2A) 9031  
87 1HIO 1 A HISTONE H2A 9031  
88 4LD9 3 C, G Histone H2A 8355  
89 3O62 3 C, G Histone H2A type 1 8355  
90 4X23 5 C, G, M, Q Histone H2A UNP RESIDUES 16-117 7227  
91 3W97 3 C, G Histone H2A type 1-B/E 9606  
92 2FJ7 5 C, G histone H2A 8355  
93 3W98 3 C, G Histone H2A type 1-B/E 9606  
94 3AN2 3 C, G Histone H2A type 1-B/E 9606  
95 3B6F 5 C, G Histone H2A 8355  
96 3B6G 5 C, G Histone H2A 8355  
97 3KXB 3 C, G Histone H2A 8355  
98 3KWQ 3 C, G Histone H2A UNP residues 15-121 8355  
99 1ZBB 5 C, G, c, g Histone H2A.1 8355  
100 2XQL 1 A, C, E, G, I HISTONE H2A-IV RESIDUES 16-106 9031  
101 3C9K 1 A, E Histone H2A-IV 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 15 1023
95% 33 97 83
90% 33 100 85
70% 33 100 104
50% 34 103 138
40% 34 103 167
30% 34 103 191
Entity #2: Chains: B,F - Histone H4 protein, length: 106 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 30 84 68
95% 34 99 81
90% 35 103 80
70% 35 103 98
50% 35 103 134
40% 35 103 162
30% 35 103 187
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 23 564
95% 24 86 87
90% 27 92 90
70% 27 95 103
50% 29 101 131
40% 29 101 160
30% 29 101 185
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 22 624
95% 25 86 88
90% 25 88 96
70% 27 94 109
50% 27 94 149
40% 27 94 177
30% 27 94 197
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.