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Crystal structure of catalytic domain of G9A with MS012
Analyse Crystal structure of catalytic domain of G9A with MS012 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TTF
- Type
- protein
- Length
- 1,059 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, 7KZ, ZN, UNX, CL
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 12% 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 | 265 | 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 | 265 | 13% helix, 25% strand | Q96KQ7 |
| D | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 261 | 10% helix, 26% strand | Q96KQ7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- 7KZ · N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-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 · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.81 | 0.83 | 73 | UNX |
| 2 | 1057 | 0.80 | 0.81 | 72 | empty |
| 3 | 463 | 0.71 | 0.81 | 80 | CL, UNX |
| 4 | 657 | 0.68 | 0.76 | 67 | SAM, 7KZ |
| 5 | 503 | 0.67 | 0.78 | 55 | SAM, 7KZ |
Interfaces
5 interfaces between chains.
- A–C · 1204 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1164 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 351 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 264 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5TTF · Crystal structure of catalytic domain of G9a with MS012 · 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 5TTF · PDBe 5TTF · UniProt Q96KQ7
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