MolNFT v1 · #153278 · protein + DNA
Cryo-EM structure of human DOT1L in complex with an H2B- monoubiquitinated nucleosome
6J99 · Histone H3: “Cryo-EM structure of human DOT1L in complex with an H2B- monoubiquitinated nucleosome”. Electron microscopy, 1 ligand (SAH), 20 pockets (best druggability 0.85). MolNFT v1 #153278 on GenesisL1: 3D structure, binding…
- PDB
- 6J99
- Type
- protein + DNA
- Length
- 1,452 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B 1.1; DNA (144-mer); DNA (145-mer)…
- EC
- 2.1.1.43
- UniProt
- A0A310TTQ1, P62799, Q6AZJ8, P02281, P62979, Q8TEK3
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 11 distinct chains · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3 | protein | 97 | 66% helix, 4% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 86 | 59% helix, 7% strand | P62799 |
| C | Histone H2A | protein | 108 | 56% helix, 5% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 94 | 72% helix, 4% strand | P02281 |
| F | Histone H4 | protein | 81 | 59% helix, 5% strand | P62799 |
| G | Histone H2A | protein | 105 | 53% helix, 6% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 95 | 74% helix, 4% strand | P02281 |
| I | DNA (144-mer) | dna | 144 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| L | Ubiquitin | protein | 76 | 16% helix, 20% strand | P62979 |
| K | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 324 | 43% helix, 8% strand | Q8TEK3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains 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 | 918 | 0.85 | 0.87 | 117 | empty |
| 2 | 663 | 0.85 | 0.89 | 85 | SAH |
| 3 | 496 | 0.77 | 0.85 | 62 | empty |
| 4 | 998 | 0.74 | 0.78 | 79 | empty |
| 5 | 1041 | 0.74 | 0.77 | 82 | empty |
Interfaces
44 interfaces between chains.
- I–J · 6496 Ų buried · 660 hydrogen bonds · nucleic-nucleic
- A–B · 2573 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2568 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2556 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2529 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6J99 · Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome · the same entry in another collection · chain H against H, 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 A0A310TTQ1
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt P62979
- Every structure of UniProt Q8TEK3
- Elsewhere: RCSB PDB 6J99 · PDBe 6J99 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P62979 · UniProt Q8TEK3
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