Research workbench
Crystal structure of N-methyl transferase from plasmodium knowlesi complexed with S-adenosyl methionine
Analyse Crystal structure of N-methyl transferase from plasmodium knowlesi complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IV8
- Type
- protein
- Length
- 490 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
- B3L8G9
- Ligands
- SAM
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoethanolamine N-METHYLTRANSFERASE,PUTATIVE (EC 2.1.1.103) | protein | 245 | 52% helix, 22% strand | B3L8G9 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.79 | 0.82 | 65 | SAM |
| 2 | 814 | 0.78 | 0.82 | 64 | SAM |
| 3 | 89 | 0.36 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4IV8 · Crystal structure of N-methyl transferase from Plasmodium knowlesi complexed with… · the same entry in another collection · chain B against B, 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 B3L8G9
- Elsewhere: RCSB PDB 4IV8 · PDBe 4IV8 · UniProt B3L8G9
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