Research workbench
Arabidopsis thaliana phosphoethanolamine N-methyltransferase 2 (ATPMT2) in complex with sah
Analyse Arabidopsis thaliana phosphoethanolamine N-methyltransferase 2 (ATPMT2) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WP5
- Type
- protein
- Length
- 925 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomethylethanolamine N-methyltransferase 2
- EC
- 2.1.1.-
- UniProt
- Q944H0
- Ligands
- SAH
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphomethylethanolamine N-methyltransferase 2 (EC 2.1.1.-) | protein | 463 | 43% helix, 24% strand | Q944H0 |
| B | Phosphomethylethanolamine N-methyltransferase 2 (EC 2.1.1.-) | protein | 462 | 43% helix, 24% strand | Q944H0 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.86 | 0.87 | 121 | SAH |
| 2 | 413 | 0.84 | 0.92 | 56 | empty |
| 3 | 610 | 0.75 | 0.81 | 56 | empty |
| 4 | 636 | 0.73 | 0.80 | 60 | empty |
| 5 | 405 | 0.72 | 0.83 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 3621 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5WP5 · Arabidopsis thaliana phosphoethanolamine N-methyltransferase 2 (AtPMT2) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q944H0 · AlphaFold monomer V2.0 prediction for phosphomethylethanolamine N-methyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.53
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 Q944H0
- Elsewhere: RCSB PDB 5WP5 · PDBe 5WP5 · UniProt Q944H0
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