Research workbench
Crystal structure of N-methyl transferase (pmt-2) from caenorhabditis elegant complexed with S-adenosyl homocysteine and phosphoethanolamine
Analyse Crystal structure of N-methyl transferase (pmt-2) from caenorhabditis elegant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4INE
- Type
- protein
- Length
- 859 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein pmt-2
- UniProt
- Q22993
- Ligands
- SAH, OPE
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein pmt-2 | protein | 431 | 44% helix, 23% strand | Q22993 |
| B | Protein pmt-2 | protein | 428 | 44% helix, 23% strand | Q22993 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- OPE · Phosphoric acid mono-(2-amino-ethyl) ester · 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
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.85 | 0.88 | 90 | empty |
| 2 | 176 | 0.78 | 0.93 | 36 | SAH |
| 3 | 164 | 0.76 | 0.92 | 35 | SAH |
| 4 | 130 | 0.47 | 0.78 | 20 | empty |
| 5 | 153 | 0.47 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1233 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4INE · Crystal structure of N-methyl transferase (PMT-2) from Caenorhabditis elegant complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- Q22993 · AlphaFold monomer V2.0 prediction for phosphoethanolamine methyltransferase (Q22993) · a predicted model of the same protein · 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 Q22993
- Elsewhere: RCSB PDB 4INE · PDBe 4INE · UniProt Q22993
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