MolNFT v1 · #123410 · protein
Structure of G9A set-domain with histone H3K9M peptide and excess sah
5JJ0 · Histone-lysine N-methyltransferase EHMT2: “Structure of G9A set-domain with histone H3K9M peptide and excess sah”. X-ray diffraction, 2 ligands (SAM, ZN), 10 pockets (best druggability 0.80). MolNFT v1 #123410 on GenesisL1: 3D…
- PDB
- 5JJ0
- Type
- protein
- Length
- 557 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT2; Histone H3K9M mutant peptide
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q96KQ7
- Ligands
- SAM, ZN
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 273 | 13% helix, 25% strand | Q96KQ7 |
| F | Histone H3K9M mutant peptide | protein | 8 | 0% helix, 13% strand | — |
| B | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 267 | 13% helix, 26% strand | Q96KQ7 |
| G | Histone H3K9M mutant peptide | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, F, B
- 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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.80 | 0.81 | 72 | empty |
| 2 | 237 | 0.56 | 0.78 | 30 | SAM |
| 3 | 212 | 0.55 | 0.78 | 24 | SAM |
| 4 | 62 | 0.39 | 0.80 | 19 | empty |
| 5 | 97 | 0.38 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1220 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 756 Ų buried · 18 hydrogen bonds · protein-protein
- B–G · 750 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5JJ0 · Structure of G9a SET-domain with Histone H3K9M peptide and excess SAH · the same entry in another collection · chain A against A, 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 B 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 5JJ0 · PDBe 5JJ0 · UniProt Q96KQ7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.