MolNFT v1 · #158075 · protein + DNA
Active state DOT1L bound to the H2B-ubiquitinated nucleosome, 2-to-1 complex
6NJ9 · Histone H3.2: “Active state DOT1L bound to the H2B-ubiquitinated nucleosome, 2-to-1 complex”. Electron microscopy, 1 ligand (SAM), 20 pockets (best druggability 0.82). MolNFT v1 #158075 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NJ9
- Type
- protein + DNA
- Length
- 1,882 residues
- Chains
- 14
- 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; 601 DNA strand 1; 601 DNA…
- EC
- 2.1.1.360
- UniProt
- P84233, P62799, P06897, P02281, Q8TEK3, P0CG47
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 99 | 65% helix, 2% strand | P84233 |
| B, F | Histone H4 | protein | 88 | 56% helix, 6% strand | P62799 |
| C, G | Histone H2A type 1 | protein | 109 | 49% helix, 6% strand | P06897 |
| D, H | Histone H2B 1.1 | protein | 95 | 73% helix, 4% strand | P02281 |
| I | 601 DNA strand 1 | dna | 146 | — | — |
| J | 601 DNA strand 2 | dna | 146 | — | — |
| K, M | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.360) | protein | 329 | 40% helix, 10% strand | Q8TEK3 |
| L, N | Ubiquitin | protein | 75 | 24% helix, 31% strand | P0CG47 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains E, K, A, M
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 | 968 | 0.82 | 0.84 | 93 | empty |
| 2 | 1112 | 0.82 | 0.83 | 107 | empty |
| 3 | 559 | 0.76 | 0.83 | 50 | empty |
| 4 | 490 | 0.75 | 0.83 | 51 | empty |
| 5 | 200 | 0.74 | 0.90 | 38 | SAM |
Interfaces
45 interfaces between chains.
- I–J · 6651 Ų buried · 503 hydrogen bonds · nucleic-nucleic
- E–F · 2650 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2644 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2548 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2545 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 6NJ9 · Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex · the same entry in another collection · chain K against K, 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 Q8TEK3
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6NJ9 · PDBe 6NJ9 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt Q8TEK3 · UniProt P0CG47
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