MolNFT v1 · #158210 · protein + DNA
Structure of DOT1L-H2BK120UB nucleosome complex
6NN6 · Histone H3.2: “Structure of DOT1L-H2BK120UB nucleosome complex”. Electron microscopy, 20 pockets (best druggability 0.75). MolNFT v1 #158210 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NN6
- Type
- protein + DNA
- Length
- 1,439 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; DNA (145-mer)…
- EC
- 2.1.1.43
- UniProt
- P84233, P62799, P06897, P02281, Q8TEK3, F5H388
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 11 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 97 | 62% helix, 3% strand | P84233 |
| B | Histone H4 | protein | 80 | 60% helix, 8% strand | P62799 |
| C | Histone H2A type 1 | protein | 104 | 40% helix, 6% strand | P06897 |
| D, H | Histone H2B 1.1 | protein | 93 | 71% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 97 | 57% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 78 | 55% helix, 8% strand | P62799 |
| G | Histone H2A type 1 | protein | 105 | 48% helix, 3% strand | P06897 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| K | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 328 | 38% helix, 12% strand | Q8TEK3 |
| L | Ubiquitin | protein | 74 | 19% helix, 35% strand | F5H388 |
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 | 360 | 0.75 | 0.86 | 52 | empty |
| 2 | 496 | 0.74 | 0.83 | 50 | empty |
| 3 | 709 | 0.74 | 0.80 | 61 | empty |
| 4 | 636 | 0.72 | 0.80 | 54 | empty |
| 5 | 456 | 0.67 | 0.79 | 43 | empty |
Interfaces
41 interfaces between chains.
- I–J · 6896 Ų buried · 904 hydrogen bonds · nucleic-nucleic
- C–D · 2581 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2547 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2538 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2534 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6NN6 · Structure of Dot1L-H2BK120ub nucleosome complex · 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 P06897
- Every structure of UniProt P02281
- Every structure of UniProt Q8TEK3
- Every structure of UniProt F5H388
- Elsewhere: RCSB PDB 6NN6 · PDBe 6NN6 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt Q8TEK3 · UniProt F5H388
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