MolNFT v1 · #79930 · protein
Crystal structure of rat native liver glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate
3THR: “Crystal structure of rat native liver glycine N-methyltransferase complexed with 5-methyltetrahydrofolate…”. X-ray diffraction, 3 ligands (ACE, C2F, TAM), 16 pockets (best druggability 0.84). MolNFT v1 #79930 on GenesisL1: 3D…
- PDB
- 3THR
- Type
- protein
- Length
- 1,141 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, C2F, TAM
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 286 | 30% helix, 30% strand | P13255 |
| B | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 286 | 31% helix, 30% strand | P13255 |
| C | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 284 | 31% helix, 30% strand | P13255 |
| D | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 285 | 31% helix, 29% strand | P13255 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, C, D, B
- C2F · 5-methyl-5,6,7,8-tetrahydrofolic acid · ligand · 4 copies · chains A, B, C, D
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 3 copies · chains A, B, C, 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 | 298 | 0.84 | 0.95 | 54 | TAM |
| 2 | 248 | 0.83 | 0.96 | 41 | TAM |
| 3 | 561 | 0.81 | 0.87 | 82 | ACE, TAM, C2F |
| 4 | 586 | 0.81 | 0.86 | 90 | ACE, C2F |
| 5 | 415 | 0.78 | 0.87 | 56 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2279 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2273 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 1108 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1093 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 185 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3THR · 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 D 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 3THR · PDBe 3THR · UniProt P13255
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.