MolNFT v1 · #158253 · protein + DNA
Poised-state DOT1L bound to the H2B-ubiquitinated nucleosome
6NOG · Histone H3.2: “Poised-state DOT1L bound to the H2B-ubiquitinated nucleosome”. Electron microscopy, 20 pockets (best druggability 0.73). MolNFT v1 #158253 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NOG
- Type
- protein + DNA
- Length
- 1,416 residues
- Chains
- 12
- 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; Ubiquitin; Histone-lysine…
- EC
- 2.1.1.43
- UniProt
- P84233, P62799, P06897, P02281, J3QS39, Q8TEK3
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 11 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 96 | 68% helix, 1% strand | P84233 |
| B | Histone H4 | protein | 78 | 59% helix, 4% strand | P62799 |
| F | Histone H4 | protein | 82 | 61% helix, 4% strand | P62799 |
| C | Histone H2A type 1 | protein | 104 | 55% helix, 5% strand | P06897 |
| G | Histone H2A type 1 | protein | 105 | 56% helix, 6% strand | P06897 |
| D | Histone H2B 1.1 | protein | 93 | 68% helix, 4% strand | P02281 |
| H | Histone H2B 1.1 | protein | 94 | 66% helix, 4% strand | P02281 |
| L | Ubiquitin | protein | 74 | 26% helix, 34% strand | J3QS39 |
| K | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 302 | 44% helix, 15% strand | Q8TEK3 |
| I | 601 DNA strand 1 | dna | 146 | — | — |
| J | 601 DNA strand 2 | dna | 146 | — | — |
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 | 937 | 0.73 | 0.77 | 70 | empty |
| 2 | 281 | 0.72 | 0.87 | 29 | empty |
| 3 | 263 | 0.71 | 0.86 | 37 | empty |
| 4 | 227 | 0.70 | 0.87 | 43 | empty |
| 5 | 245 | 0.70 | 0.86 | 38 | empty |
Interfaces
40 interfaces between chains.
- I–J · 6482 Ų buried · 499 hydrogen bonds · nucleic-nucleic
- C–D · 2660 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2563 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 2562 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2454 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6NOG · Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome · the same entry in another collection · chain J against J, 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 J3QS39
- Every structure of UniProt Q8TEK3
- Elsewhere: RCSB PDB 6NOG · PDBe 6NOG · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt J3QS39 · UniProt Q8TEK3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.