MolNFT v1 · #151334 · protein + DNA
Structure of an H1-bound 6-nucleosome array
6HKT · Histone H3.1: “Structure of an H1-bound 6-nucleosome array”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #151334 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HKT
- Type
- protein + DNA
- Length
- 6,792 residues
- Chains
- 50
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (1122-mer)
- UniProt
- P68431, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 9 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, e, K, o, U, y | Histone H3.1 | protein | 97 | 66% helix, 4% strand | P68431 |
| B, F, b, f, L, P, l, p, V, Z, v, z | Histone H4 | protein | 82 | 61% helix, 9% strand | P62805 |
| C, g, M, q, W, 2 | Histone H2A type 1-B/E | protein | 103 | 59% helix, 7% strand | P04908 |
| D, h, N, r, X, 3 | Histone H2B type 1-J | protein | 96 | 72% helix, 4% strand | P06899 |
| E, a, O, k, Y, u | Histone H3.1 | protein | 98 | 65% helix, 4% strand | P68431 |
| G, c, Q, m, 0, w | Histone H2A type 1-B/E | protein | 105 | 52% helix, 7% strand | P04908 |
| H, d, R, n, 1, x | Histone H2B type 1-J | protein | 95 | 74% helix, 4% strand | P06899 |
| I | DNA (1122-mer) | dna | 1122 | — | — |
| J | DNA (1122-mer) | dna | 1122 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.84 | 0.86 | 109 | empty |
| 2 | 1085 | 0.84 | 0.85 | 133 | empty |
| 3 | 840 | 0.80 | 0.83 | 103 | empty |
| 4 | 818 | 0.80 | 0.83 | 97 | empty |
| 5 | 418 | 0.79 | 0.88 | 57 | empty |
Interfaces
229 interfaces between chains.
- I–J · 51094 Ų buried · 5,157 hydrogen bonds · nucleic-nucleic
- 2–3 · 2714 Ų buried · 30 hydrogen bonds · protein-protein
- q–r · 2705 Ų buried · 31 hydrogen bonds · protein-protein
- M–N · 2697 Ų buried · 28 hydrogen bonds · protein-protein
- W–X · 2695 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6HKT · Structure of an H1-bound 6-nucleosome array · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 6HKT · PDBe 6HKT · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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