Research workbench
Crystal structure of mouse nicotinamide N-methyltransferase (nnmt) bound with end product, 1-methyl nicotinamide (mna)
Analyse Crystal structure of mouse nicotinamide N-methyltransferase (nnmt) bound with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XVK
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide N-methyltransferase
- EC
- 2.1.1.1
- UniProt
- O55239
- Ligands
- SAH, 8GC
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 261 | 38% helix, 25% strand | O55239 |
| B | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 258 | 38% helix, 23% strand | O55239 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- 8GC · 3-carbamoyl-1-methylpyridin-1-ium · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.81 | 0.94 | 41 | SAH, 8GC |
| 2 | 199 | 0.80 | 0.94 | 38 | SAH, 8GC |
| 3 | 411 | 0.61 | 0.76 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 627 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5XVK · Crystal structure of mouse Nicotinamide N-methyltransferase (NNMT) bound with end… · the same entry in another collection · chain A against A, TM-score 1.00
- O55239 · AlphaFold monomer V2.0 prediction for nicotinamide N-methyltransferase (O55239) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O55239
- Elsewhere: RCSB PDB 5XVK · PDBe 5XVK · UniProt O55239
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