MolNFT v1 · #31587 · protein
Crystal structure of H176N mutant of human glycine N-methyltransferase
2AZT: “Crystal structure of H176N mutant of human glycine N-methyltransferase”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.79). MolNFT v1 #31587 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2AZT
- Type
- protein
- Length
- 553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine N-methyltransferase
- EC
- 2.1.1.20
- UniProt
- Q14749
- Ligands
- CL
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 276 | 32% helix, 28% strand | Q14749 |
| B | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 277 | 31% helix, 29% strand | Q14749 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B
- BME · Beta-mercaptoethanol · additive · 5 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.79 | 0.87 | 67 | CIT |
| 2 | 413 | 0.78 | 0.87 | 66 | CIT |
| 3 | 455 | 0.78 | 0.86 | 59 | empty |
| 4 | 111 | 0.37 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2381 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (additive adduct).
Compared structures
- 2AZT · Crystal structure of H176N mutant of human Glycine N-Methyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
- Q14749 · AlphaFold monomer V2.0 prediction for glycine N-methyltransferase (Q14749) · a predicted model of the same protein · chain B 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 Q14749
- Elsewhere: RCSB PDB 2AZT · PDBe 2AZT · UniProt Q14749
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