MolNFT v1 · #158937 · protein + DNA
DOT1L bound to the H2BK120 ubiquitinated nucleosome
6O96 · Histone H3.2: “DOT1L bound to the H2BK120 ubiquitinated nucleosome”. Electron microscopy, 1 ligand (SAH), 20 pockets (best druggability 0.82). MolNFT v1 #158937 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O96
- Type
- protein + DNA
- Length
- 1,453 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (146-mer); Histone-lysine…
- EC
- 2.1.1.43
- UniProt
- P84233, P62799, Q6AZJ8, P02281, Q8TEK3, J3QS39
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 98 | 63% helix, 4% strand | P84233 |
| B, F | Histone H4 | protein | 84 | 56% helix, 7% strand | P62799 |
| C, G | Histone H2A | protein | 107 | 50% helix, 6% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 93 | 73% helix, 4% strand | P02281 |
| I | DNA (146-mer) | dna | 146 | — | — |
| J | DNA (146-mer) | dna | 146 | — | — |
| K | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 321 | 43% helix, 11% strand | Q8TEK3 |
| L | Polyubiquitin-B | protein | 76 | 20% helix, 32% strand | J3QS39 |
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 | 913 | 0.82 | 0.84 | 99 | empty |
| 2 | 737 | 0.77 | 0.81 | 58 | empty |
| 3 | 288 | 0.72 | 0.86 | 31 | empty |
| 4 | 491 | 0.72 | 0.81 | 47 | empty |
| 5 | 191 | 0.71 | 0.89 | 26 | empty |
Interfaces
41 interfaces between chains.
- I–J · 6484 Ų buried · 540 hydrogen bonds · nucleic-nucleic
- E–F · 2600 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2571 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 2557 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2535 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6O96 · Dot1L bound to the H2BK120 Ubiquitinated 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 Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt Q8TEK3
- Every structure of UniProt J3QS39
- Elsewhere: RCSB PDB 6O96 · PDBe 6O96 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt Q8TEK3 · UniProt J3QS39
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