MolNFT v1 · #158318 · protein + DNA
Active state DOT1L bound to the H2B-ubiquitinated nucleosome, 1-to-1 complex
6NQA · 601 DNA strand 1: “Active state DOT1L bound to the H2B-ubiquitinated nucleosome, 1-to-1 complex”. Electron microscopy, 1 ligand (SAM), 20 pockets (best druggability 0.83). MolNFT v1 #158318 on GenesisL1: 3D structure, binding sites…
- PDB
- 6NQA
- Type
- protein + DNA
- Length
- 1,456 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 601 DNA strand 1; 601 DNA strand 2; Histone H4; Histone H2A type 1; Histone H2B 1.1…
- EC
- 2.1.1.43
- UniProt
- P62799, P06897, P02281, Q8TEK3, P0CG48, P84233
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 12 distinct chains · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | 601 DNA strand 1 | dna | 146 | — | — |
| J | 601 DNA strand 2 | dna | 146 | — | — |
| F | Histone H4 | protein | 88 | 57% helix, 2% strand | P62799 |
| G | Histone H2A type 1 | protein | 108 | 45% helix, 5% strand | P06897 |
| H | Histone H2B 1.1 | protein | 93 | 65% helix, 3% strand | P02281 |
| K | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 328 | 40% helix, 9% strand | Q8TEK3 |
| L | Ubiquitin | protein | 75 | 25% helix, 33% strand | P0CG48 |
| E | Histone H3.2 | protein | 97 | 59% helix, 1% strand | P84233 |
| A | Histone H3.2 | protein | 97 | 63% helix, 0% strand | P84233 |
| D | Histone H2B 1.1 | protein | 92 | 64% helix, 3% strand | P02281 |
| C | Histone H2A type 1 | protein | 106 | 43% helix, 4% strand | P06897 |
| B | Histone H4 | protein | 80 | 64% helix, 3% strand | P62799 |
Ligands and binding sites
- SAM · S-adenosylmethionine · 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 | 1006 | 0.83 | 0.84 | 100 | empty |
| 2 | 832 | 0.80 | 0.83 | 88 | empty |
| 3 | 281 | 0.75 | 0.88 | 41 | SAM |
| 4 | 509 | 0.73 | 0.82 | 39 | empty |
| 5 | 261 | 0.72 | 0.87 | 31 | empty |
Interfaces
43 interfaces between chains.
- I–J · 6542 Ų buried · 491 hydrogen bonds · nucleic-nucleic
- F–E · 2733 Ų buried · 19 hydrogen bonds · protein-protein
- D–C · 2673 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 2620 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2591 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 6NQA · Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex · the same entry in another collection · chain A against A, 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 P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Every structure of UniProt Q8TEK3
- Every structure of UniProt P0CG48
- Every structure of UniProt P84233
- Elsewhere: RCSB PDB 6NQA · PDBe 6NQA · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt Q8TEK3 · UniProt P0CG48 · UniProt P84233
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