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Crystal structure of N-methyl transferase from plasmodium vivax complexed with S-adenosyl methionine and phosphate
Analyse Crystal structure of N-methyl transferase from plasmodium vivax complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IV0
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoethanolamine N-methyltransferase, putative
- EC
- 2.1.1.103
- UniProt
- A5K867
- Ligands
- SAM, PO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoethanolamine N-methyltransferase, putative (EC 2.1.1.103) | protein | 263 | 50% helix, 20% strand | A5K867 |
| B | Phosphoethanolamine N-methyltransferase, putative (EC 2.1.1.103) | protein | 260 | 49% helix, 20% strand | A5K867 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · chains B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.82 | 0.95 | 51 | PO4, SAM |
| 2 | 688 | 0.71 | 0.78 | 73 | SAM |
| 3 | 273 | 0.66 | 0.82 | 41 | PO4 |
| 4 | 122 | 0.51 | 0.81 | 23 | empty |
| 5 | 156 | 0.44 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 197 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 4IV0 · Crystal structure of N-methyl transferase from Plasmodium vivax complexed with S-adenosyl… · the same entry in another collection · chain A against A, TM-score 1.00
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 A5K867
- Elsewhere: RCSB PDB 4IV0 · PDBe 4IV0 · UniProt A5K867
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