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Co-crystal structure of mouse nicotinamide N-methyltransferase (nnmt) with small molecule analog of nicotinamide
Analyse Co-crystal structure of mouse nicotinamide N-methyltransferase (nnmt) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YJI
- Type
- protein
- Length
- 508 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, 8WO
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 256 | 39% helix, 25% strand | O55239 |
| B | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 252 | 40% helix, 25% strand | O55239 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- 8WO · 6-methoxy-1-methyl-2H-pyridine-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.82 | 0.95 | 42 | SAH, 8WO |
| 2 | 163 | 0.77 | 0.93 | 32 | SAH |
| 3 | 56 | 0.71 | 0.97 | 18 | 8WO |
| 4 | 504 | 0.63 | 0.76 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 606 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5YJI · Co-crystal structure of Mouse Nicotinamide N-methyltransferase (NNMT) with small molecule… · the same entry in another collection · chain B against B, 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 5YJI · PDBe 5YJI · UniProt O55239
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