MolNFT v1 · #179476 · protein + DNA
Active state DOT1 bound to the unacetylated H4 nucleosome
7K6P · Histone H3.2: “Active state DOT1 bound to the unacetylated H4 nucleosome”. Electron microscopy, 1 ligand (SAM), 20 pockets (best druggability 0.83). MolNFT v1 #179476 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K6P
- Type
- protein + DNA
- Length
- 1,511 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; DNA (146-mer)…
- EC
- 2.1.1.360
- UniProt
- P84233, P62799, P06897, P02281, Q04089, P0CG48
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 10 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 98 | 63% helix, 2% strand | P84233 |
| B | Histone H4 | protein | 86 | 53% helix, 5% strand | P62799 |
| C, G | Histone H2A type 1 | protein | 107 | 53% helix, 6% strand | P06897 |
| D, H | Histone H2B 1.1 | protein | 93 | 73% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 95 | 65% helix, 2% strand | P84233 |
| F | Histone H4 | protein | 87 | 53% helix, 5% strand | P62799 |
| I | DNA (146-mer) | dna | 146 | — | — |
| J | DNA (146-mer) | dna | 146 | — | — |
| K | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.360) | protein | 377 | 42% helix, 15% strand | Q04089 |
| L | Ubiquitin | protein | 76 | 25% helix, 33% strand | P0CG48 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 970 | 0.83 | 0.84 | 94 | empty |
| 2 | 914 | 0.81 | 0.83 | 92 | empty |
| 3 | 186 | 0.75 | 0.91 | 41 | SAM |
| 4 | 318 | 0.74 | 0.86 | 40 | empty |
| 5 | 278 | 0.73 | 0.87 | 38 | empty |
Interfaces
45 interfaces between chains.
- I–J · 6542 Ų buried · 557 hydrogen bonds · nucleic-nucleic
- A–B · 2643 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2554 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2531 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2526 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7K6P · Active state Dot1 bound to the unacetylated H4 nucleosome · the same entry in another collection · chain L against L, 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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Every structure of UniProt Q04089
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 7K6P · PDBe 7K6P · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt Q04089 · UniProt P0CG48
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