Research workbench
Crystal structure of R175K mutant glycine N-methyltransferase complexed with S-adenosylhomocysteine
Analyse Crystal structure of R175K mutant glycine N-methyltransferase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D2H
- Type
- protein
- Length
- 1,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine N-methyltransferase
- EC
- 2.1.1.20
- UniProt
- P13255
- Ligands
- SAH
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 252 | 32% helix, 31% strand | P13255 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.69 | 0.85 | 26 | empty |
| 2 | 227 | 0.68 | 0.85 | 24 | empty |
| 3 | 503 | 0.68 | 0.79 | 52 | SAH |
| 4 | 541 | 0.68 | 0.78 | 50 | SAH |
| 5 | 515 | 0.67 | 0.77 | 52 | SAH |
Interfaces
4 interfaces between chains.
- B–D · 545 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 511 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 481 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 478 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1D2H · Crystal structure of R175K mutant glycine N-methyltransferase complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- P13255 · AlphaFold monomer V2.0 prediction for glycine N-methyltransferase (P13255) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P13255
- Elsewhere: RCSB PDB 1D2H · PDBe 1D2H · UniProt P13255
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