MolNFT v1 · #138626 · protein
Arabidopsis thaliana phosphoethanolamine N-methyltransferase 1 (ATPMT1, xioptl) in complex with sah and phosphocholine
5WP4: “Arabidopsis thaliana phosphoethanolamine N-methyltransferase 1 (ATPMT1, xioptl) in complex with sah and…”. X-ray diffraction, 2 ligands (SAH, PC), 5 pockets (best druggability 0.85). MolNFT v1 #138626 on GenesisL1: 3D structure…
- PDB
- 5WP4
- Type
- protein
- Length
- 485 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoethanolamine N-methyltransferase 1
- EC
- 2.1.1.103
- UniProt
- Q9FR44
- Ligands
- SAH, PC
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoethanolamine N-methyltransferase 1 (EC 2.1.1.103) | protein | 485 | 44% helix, 23% strand | Q9FR44 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A
- PC · Phosphocholine · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.85 | 0.97 | 49 | SAH, PC |
| 2 | 178 | 0.79 | 0.94 | 35 | SAH |
| 3 | 197 | 0.61 | 0.82 | 35 | empty |
| 4 | 121 | 0.54 | 0.82 | 29 | PC |
| 5 | 70 | 0.35 | 0.76 | 15 | empty |
Compared structures
- 5WP4 · Arabidopsis thaliana phosphoethanolamine N-methyltransferase 1 (AtPMT1, XIOPTL) in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FR44 · AlphaFold monomer V2.0 prediction for phosphoethanolamine N-methyltransferase 1 (Q9FR44) · a predicted model of the same protein · chain A against A, TM-score 0.73
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 Q9FR44
- Elsewhere: RCSB PDB 5WP4 · PDBe 5WP4 · UniProt Q9FR44
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