MolNFT v1 · #79931 · protein
Crystal structure of rat native liver glycine N-methyltransferase complexed with 5-methyltetrahydrofolate pentaglutamate
3THS: “Crystal structure of rat native liver glycine N-methyltransferase complexed with 5-methyltetrahydrofolate…”. X-ray diffraction, 4 ligands (ACE, GGL, 03O), 16 pockets (best druggability 0.83). MolNFT v1 #79931 on GenesisL1: 3D…
- PDB
- 3THS
- Type
- protein
- Length
- 1,135 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
- ACE, GGL, 03O, TAM
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 283 | 31% helix, 30% strand | P13255 |
| B | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 285 | 31% helix, 31% strand | P13255 |
| C | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 284 | 32% helix, 29% strand | P13255 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, C, D, B
- GGL · Gamma-L-glutamic acid · ligand · 4 copies · chains A, D, B
- 03O · 4-({[(6S)-2-amino-5-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoic acid · ligand · 2 copies · chains A, B, C, D
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A, B
- BME · Beta-mercaptoethanol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.83 | 0.94 | 52 | TAM |
| 2 | 272 | 0.83 | 0.94 | 52 | empty |
| 3 | 639 | 0.82 | 0.86 | 92 | 03O, GGL |
| 4 | 671 | 0.81 | 0.86 | 97 | ACE, 03O, GGL |
| 5 | 473 | 0.79 | 0.87 | 56 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2308 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2282 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1067 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1059 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 177 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand, additive adduct).
Compared structures
- 3THS · Crystal structure of rat native liver 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 0.88
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 3THS · PDBe 3THS · UniProt P13255
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