MolNFT v1 · #20251 · protein
Crystal structure of mouse glycine N-methyltransferase (tetragonal form)
1R8X: “Crystal structure of mouse glycine N-methyltransferase (tetragonal form)”. X-ray diffraction, 7 pockets (best druggability 0.83). MolNFT v1 #20251 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1R8X
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine N-methyltransferase
- UniProt
- Q9QXF8
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine N-methyltransferase | protein | 283 | 30% helix, 28% strand | Q9QXF8 |
| B | Glycine N-methyltransferase | protein | 284 | 30% helix, 27% strand | Q9QXF8 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, 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 | 287 | 0.83 | 0.94 | 43 | TRS |
| 2 | 264 | 0.82 | 0.93 | 43 | TRS |
| 3 | 537 | 0.77 | 0.84 | 63 | empty |
| 4 | 141 | 0.45 | 0.76 | 25 | BME |
| 5 | 146 | 0.44 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2342 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 1R8X · Crystal Structure of Mouse Glycine N-Methyltransferase (Tetragonal Form) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9QXF8 · AlphaFold monomer V2.0 prediction for glycine N-methyltransferase (Q9QXF8) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q9QXF8
- Elsewhere: RCSB PDB 1R8X · PDBe 1R8X · UniProt Q9QXF8
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