MolNFT v1 · #153687 · protein + DNA
Cryo-EM structure of DOT1L bound to unmodified nucleosome
6JM9 · DNA strand I: “Cryo-EM structure of DOT1L bound to unmodified nucleosome”. Electron microscopy, 1 ligand (SAM), 20 pockets (best druggability 0.82). MolNFT v1 #153687 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JM9
- Type
- protein + DNA
- Length
- 1,340 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA strand I; DNA strand J; Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1…
- EC
- 2.1.1.43
- UniProt
- P84233, P62799, Q6AZJ8, P02281, Q8TEK3
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 9 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA strand I | dna | 123 | — | — |
| J | DNA strand J | dna | 123 | — | — |
| A, E | Histone H3.2 | protein | 98 | 65% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 61% helix, 9% strand | P62799 |
| C | Histone H2A | protein | 107 | 56% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 94 | 74% helix, 4% strand | P02281 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62799 |
| G | Histone H2A | protein | 106 | 57% helix, 7% strand | Q6AZJ8 |
| X | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 328 | 41% helix, 14% strand | Q8TEK3 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.82 | 0.83 | 86 | empty |
| 2 | 470 | 0.77 | 0.86 | 58 | empty |
| 3 | 391 | 0.75 | 0.85 | 54 | empty |
| 4 | 581 | 0.73 | 0.81 | 46 | empty |
| 5 | 589 | 0.73 | 0.80 | 48 | empty |
Interfaces
42 interfaces between chains.
- I–J · 5411 Ų buried · 422 hydrogen bonds · nucleic-nucleic
- C–D · 2640 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2597 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2572 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2572 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
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 Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt Q8TEK3
- Elsewhere: RCSB PDB 6JM9 · PDBe 6JM9 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt Q8TEK3
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