MolNFT v1 · #136967 · protein
Crystal structure of catalytic domain of glp with MS0105
5V9J · Histone-lysine N-methyltransferase EHMT1: “Crystal structure of catalytic domain of glp with MS0105”. X-ray diffraction, 5 ligands (SAM, 90P, ZN), 7 pockets (best druggability 0.80). MolNFT v1 #136967 on GenesisL1: 3D structure…
- PDB
- 5V9J
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT1
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9H9B1
- Ligands
- SAM, 90P, ZN, UNX, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 257 | 10% helix, 27% strand | Q9H9B1 |
| B | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 259 | 10% helix, 26% strand | Q9H9B1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- 90P · N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- UNX · Unknown atom or ion · ion · 13 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.80 | 0.82 | 91 | CL, UNX |
| 2 | 483 | 0.66 | 0.78 | 58 | SAM, 90P, UNX |
| 3 | 370 | 0.63 | 0.78 | 46 | SAM, 90P |
| 4 | 96 | 0.43 | 0.79 | 21 | UNX |
| 5 | 109 | 0.40 | 0.76 | 21 | CL |
Interfaces
1 interface between chains.
- A–B · 1079 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5V9J · Crystal structure of catalytic domain of GLP with MS0105 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9H9B1 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT1 (Q9H9B1) · 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 Q9H9B1
- Elsewhere: RCSB PDB 5V9J · PDBe 5V9J · UniProt Q9H9B1
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