MolNFT v1 · #139966 · protein
Crystal structure of monkey nicotinamide N-methyltransferase (nnmt) bound with end product, 1-methyl nicotinamide (mna)
5XVQ: “Crystal structure of monkey nicotinamide N-methyltransferase (nnmt) bound with end product, 1-methyl…”. X-ray diffraction, 2 ligands (SAH, 8GC), 5 pockets (best druggability 0.80). MolNFT v1 #139966 on GenesisL1: 3D structure…
- PDB
- 5XVQ
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide N-methyltransferase (nnmt)
- UniProt
- F7ERX8
- Ligands
- SAH, 8GC
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide N-methyltransferase (nnmt) | protein | 252 | 39% helix, 27% strand | F7ERX8 |
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 · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.80 | 0.94 | 40 | SAH, 8GC |
| 2 | 155 | 0.77 | 0.94 | 30 | SAH |
| 3 | 50 | 0.68 | 0.96 | 15 | 8GC |
| 4 | 221 | 0.52 | 0.77 | 31 | empty |
| 5 | 165 | 0.50 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 410 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XVQ · Crystal structure of monkey Nicotinamide N-methyltransferase (NNMT) bound with end… · 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
- Every structure of UniProt F7ERX8
- Elsewhere: RCSB PDB 5XVQ · PDBe 5XVQ · UniProt F7ERX8
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