MolNFT v1 · #136966 · protein
Crystal structure of catalytic domain of G9A with MS0105
5V9I · Histone-lysine N-methyltransferase EHMT2: “Crystal structure of catalytic domain of G9A with MS0105”. X-ray diffraction, 4 ligands (SAM, 90P, ZN), 20 pockets (best druggability 0.80). MolNFT v1 #136966 on GenesisL1: 3D structure…
- PDB
- 5V9I
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT2
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q96KQ7
- Ligands
- SAM, 90P, ZN, UNX
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 266 | 12% helix, 26% strand | Q96KQ7 |
| B | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 268 | 13% helix, 25% strand | Q96KQ7 |
| C | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 264 | 11% helix, 26% strand | Q96KQ7 |
| D | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 265 | 12% helix, 26% strand | Q96KQ7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- 90P · N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D
- UNX · Unknown atom or ion · ion · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.80 | 0.81 | 69 | GOL |
| 2 | 1070 | 0.79 | 0.81 | 70 | GOL |
| 3 | 622 | 0.70 | 0.78 | 75 | 90P |
| 4 | 352 | 0.66 | 0.80 | 48 | SAM, 90P |
| 5 | 315 | 0.59 | 0.77 | 39 | 90P |
Interfaces
3 interfaces between chains.
- C–D · 1169 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1155 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5V9I · Crystal structure of catalytic domain of G9a with MS0105 · the same entry in another collection · chain D against D, 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 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 Q96KQ7
- Elsewhere: RCSB PDB 5V9I · PDBe 5V9I · UniProt Q96KQ7
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