Research workbench
Semet haemonchus contortus phosphoethanolamine N-methyltransferase 1 in complex with phosphoethanolamine and S-adenosylhomocysteine
Analyse Semet haemonchus contortus phosphoethanolamine N-methyltransferase 1 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KRG
- Type
- protein
- Length
- 932 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoethanolamine N-methyltransferase 1
- Ligands
- OPE, SAH, NA
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoethanolamine N-methyltransferase 1 | protein | 466 | 40% helix, 24% strand | — |
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
- NA · Sodium ion · metal · 2 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.86 | 0.87 | 115 | BOG |
| 2 | 129 | 0.80 | 0.98 | 29 | SAH |
| 3 | 125 | 0.79 | 0.97 | 29 | SAH |
| 4 | 52 | 0.49 | 0.86 | 12 | empty |
| 5 | 60 | 0.48 | 0.84 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 4KRG · SeMet Haemonchus contortus Phosphoethanolamine N-methyltransferase 1 in complex with… · 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
- Elsewhere: RCSB PDB 4KRG · PDBe 4KRG
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