MolNFT v1 · #190520 · protein + DNA
Cryo-EM structure of DOT1L and H2BK34UB-H3K79NLE nucleosome 1:1 complex
7XCR · Ubiquitin: “Cryo-EM structure of DOT1L and H2BK34UB-H3K79NLE nucleosome 1:1 complex”. Electron microscopy, 1 ligand (SAM), 20 pockets (best druggability 0.82). MolNFT v1 #190520 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7XCR
- Type
- protein + DNA
- Length
- 1,466 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Histone H4; Histone H2A; Histone H2B type 1-K; Histone-lysine…
- EC
- 2.1.1.43
- UniProt
- P0CG47, A0A672GII6, Q08AJ9, O60814, Q8TEK3, S4RAZ3
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 11 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Ubiquitin | protein | 76 | 18% helix, 32% strand | P0CG47 |
| F | Histone H4 | protein | 88 | 13% helix, 9% strand | A0A672GII6 |
| G, C | Histone H2A | protein | 108 | 50% helix, 6% strand | Q08AJ9 |
| H | Histone H2B type 1-K | protein | 92 | 73% helix, 4% strand | O60814 |
| K | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 328 | 36% helix, 12% strand | Q8TEK3 |
| E | Histone domain-containing protein | protein | 98 | 65% helix, 2% strand | S4RAZ3 |
| A | Histone domain-containing protein | protein | 99 | 64% helix, 1% strand | S4RAZ3 |
| D | Histone H2B type 1-K | protein | 94 | 74% helix, 4% strand | O60814 |
| B | Histone H4 | protein | 83 | 58% helix, 5% strand | A0A672GII6 |
| I | DNA (146-mer) | dna | 146 | — | — |
| J | DNA (146-mer) | dna | 146 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains K, E
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 | 1189 | 0.82 | 0.83 | 103 | empty |
| 2 | 867 | 0.77 | 0.80 | 90 | empty |
| 3 | 478 | 0.75 | 0.84 | 48 | empty |
| 4 | 463 | 0.74 | 0.84 | 46 | empty |
| 5 | 165 | 0.74 | 0.91 | 37 | SAM |
Interfaces
41 interfaces between chains.
- I–J · 6719 Ų buried · 832 hydrogen bonds · nucleic-nucleic
- F–E · 2662 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2603 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2603 Ų buried · 20 hydrogen bonds · protein-protein
- D–C · 2588 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 7XCR · Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex · 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 P0CG47
- Every structure of UniProt A0A672GII6
- Every structure of UniProt Q08AJ9
- Every structure of UniProt O60814
- Every structure of UniProt Q8TEK3
- Every structure of UniProt S4RAZ3
- Elsewhere: RCSB PDB 7XCR · PDBe 7XCR · UniProt P0CG47 · UniProt A0A672GII6 · UniProt Q08AJ9 · UniProt O60814 · UniProt Q8TEK3 · UniProt S4RAZ3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.