MolNFT v1 · #134321 · protein
Structure of G9A set-domain with H3K9M mutant peptide and SAM
5T0K · Histone-lysine N-methyltransferase EHMT2: “Structure of G9A set-domain with H3K9M mutant peptide and SAM”. X-ray diffraction, 2 ligands (SAM, ZN), 9 pockets (best druggability 0.80). MolNFT v1 #134321 on GenesisL1: 3D structure…
- PDB
- 5T0K
- Type
- protein
- Length
- 548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT2; H3K9 mutant peptide
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q96KQ7
- Ligands
- SAM, ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 264 | 13% helix, 24% strand | Q96KQ7 |
| B | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 265 | 15% helix, 24% strand | Q96KQ7 |
| P | H3K9 mutant peptide | protein | 9 | 0% helix, 11% strand | — |
| Q | H3K9 mutant peptide | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, P, B, Q
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.80 | 0.81 | 71 | empty |
| 2 | 188 | 0.55 | 0.79 | 27 | SAM |
| 3 | 174 | 0.54 | 0.79 | 27 | SAM |
| 4 | 116 | 0.48 | 0.80 | 21 | empty |
| 5 | 55 | 0.44 | 0.84 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1227 Ų buried · 18 hydrogen bonds · protein-protein
- B–Q · 808 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 749 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5T0K · Structure of G9a SET-domain with H3K9M mutant peptide and SAM · the same entry in another collection · chain B against B, TM-score 1.00
- Q96KQ7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT2 (Q96KQ7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q96KQ7
- Elsewhere: RCSB PDB 5T0K · PDBe 5T0K · UniProt Q96KQ7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.