MolNFT v1 · #23531 · protein
Crystal structure of histone K79 methyltransferase DOT1P from yeast
1U2Z · Histone-lysine N-methyltransferase, H3 lysine-79 specific: “Crystal structure of histone K79 methyltransferase DOT1P from yeast”. X-ray diffraction, 1 ligand (SAH), 20 pockets (best druggability 0.78). MolNFT v1 #23531 on GenesisL1…
- PDB
- 1U2Z
- Type
- protein
- Length
- 1,143 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-79 specific
- EC
- 2.1.1.43
- UniProt
- Q04089
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 379 | 41% helix, 16% strand | Q04089 |
| B | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 379 | 43% helix, 16% strand | Q04089 |
| C | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 385 | 41% helix, 16% strand | Q04089 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.78 | 0.90 | 54 | SAH |
| 2 | 583 | 0.77 | 0.83 | 82 | SAH |
| 3 | 256 | 0.76 | 0.89 | 50 | SAH |
| 4 | 50 | 0.72 | 0.99 | 18 | empty |
| 5 | 472 | 0.72 | 0.81 | 68 | empty |
Interfaces
3 interfaces between chains.
- A–C · 631 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 588 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 581 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1U2Z · Crystal structure of histone K79 methyltransferase Dot1p from yeast · the same entry in another collection · chain A against A, TM-score 1.00
- Q04089 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase, H3 lysine-79… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q04089
- Elsewhere: RCSB PDB 1U2Z · PDBe 1U2Z · UniProt Q04089
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