MolNFT v1 · #153688 · protein + DNA
Cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome
6JMA · DNA I&J: “Cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome”. Electron microscopy, 1 ligand (SAM), 20 pockets (best druggability 0.83). MolNFT v1 #153688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JMA
- Type
- protein + DNA
- Length
- 1,398 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA I&J; Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; Histone-lysine…
- EC
- 2.1.1.43
- UniProt
- P84233, P62799, Q6AZJ8, P02281, Q8TEK3, P0CG47
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J | DNA I&J | dna | 114 | — | — |
| 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 | 40% helix, 14% strand | Q8TEK3 |
| Y | Ubiquitin | protein | 76 | 20% helix, 32% strand | P0CG47 |
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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.83 | 0.86 | 102 | empty |
| 2 | 1016 | 0.82 | 0.83 | 93 | empty |
| 3 | 1019 | 0.74 | 0.77 | 97 | empty |
| 4 | 426 | 0.74 | 0.83 | 46 | empty |
| 5 | 1020 | 0.72 | 0.76 | 69 | empty |
Interfaces
44 interfaces between chains.
- I–J · 4967 Ų buried · 390 hydrogen bonds · nucleic-nucleic
- C–D · 2651 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2594 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2579 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2561 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 6JMA · cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome · the same entry in another collection · chain Y against Y, 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 Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt Q8TEK3
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6JMA · PDBe 6JMA · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt Q8TEK3 · UniProt P0CG47
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