Research workbench
Phosphoethanolamine methyltransferase from the pine wilt nematode bursaphelenchus xylophilus
Analyse Phosphoethanolamine methyltransferase from the pine wilt nematode… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WLF
- Type
- protein
- Length
- 865 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoethanolamine N-methyltransferase 1
- UniProt
- A0A1I7RPU0
- Ligands
- OPE, SAH
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoethanolamine N-methyltransferase 1 | protein | 431 | 36% helix, 26% strand | A0A1I7RPU0 |
| B | Phosphoethanolamine N-methyltransferase 1 | protein | 434 | 37% helix, 26% strand | A0A1I7RPU0 |
Ligands and binding sites
- OPE · Phosphoric acid mono-(2-amino-ethyl) ester · ligand · 2 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.79 | 0.95 | 41 | OPE, SAH |
| 2 | 165 | 0.79 | 0.95 | 42 | OPE, SAH |
| 3 | 721 | 0.70 | 0.77 | 71 | empty |
| 4 | 262 | 0.60 | 0.79 | 27 | empty |
| 5 | 132 | 0.42 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1123 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6WLF · Phosphoethanolamine Methyltransferase from the Pine Wilt Nematode Bursaphelenchus… · 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 A0A1I7RPU0
- Elsewhere: RCSB PDB 6WLF · PDBe 6WLF · UniProt A0A1I7RPU0
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