Research workbench
Crystal structure of glycine N-methyltransferase complexed with S- adenosylmethionine and acetate
Analyse Crystal structure of glycine N-methyltransferase complexed with S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KIA
- Type
- protein
- Length
- 1,100 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
- SAM
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 275 | 33% helix, 30% strand | P13255 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.76 | 0.90 | 39 | ACT, SAM |
| 2 | 186 | 0.75 | 0.91 | 24 | empty |
| 3 | 216 | 0.74 | 0.89 | 38 | ACT, SAM |
| 4 | 259 | 0.74 | 0.88 | 46 | ACT, SAM |
| 5 | 219 | 0.73 | 0.89 | 39 | ACT, SAM |
Interfaces
4 interfaces between chains.
- A–D · 608 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 580 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 488 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1KIA · Crystal structure of glycine N-methyltransferase complexed with S-adenosylmethionine and… · 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 B against A, TM-score 0.98
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 1KIA · PDBe 1KIA · UniProt P13255
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