MolNFT v1 · #72699 · protein
Complex of 6-hydroxy-L-nicotine oxidase with intermediate methylmyosmine product formed during catalytic turnover
3NGC: “Complex of 6-hydroxy-L-nicotine oxidase with intermediate methylmyosmine product formed during catalytic…”. X-ray diffraction, 4 ligands (HNL, FAD, GP7), 4 pockets (best druggability 0.86). MolNFT v1 #72699 on GenesisL1: 3D…
- PDB
- 3NGC
- Type
- protein
- Length
- 425 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-hydroxy-L-nicotine oxidase
- EC
- 1.5.3.5
- UniProt
- Q93NH4
- Ligands
- HNL, FAD, GP7, HNH
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | 6-hydroxy-L-nicotine oxidase (EC 1.5.3.5) | protein | 425 | 33% helix, 22% strand | Q93NH4 |
Ligands and binding sites
- HNL · 5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol · ligand · chains X
- FAD · Flavin-adenine dinucleotide · ligand · chains X
- GP7 · (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate · ligand · chains X
- HNH · 5-(1-methyl-4,5-dihydro-1H-pyrrol-2-yl)pyridin-2-ol · ligand · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.86 | 0.93 | 62 | HNL, FAD |
| 2 | 352 | 0.74 | 0.85 | 38 | GP7, HNH |
| 3 | 113 | 0.49 | 0.80 | 19 | empty |
| 4 | 75 | 0.35 | 0.76 | 16 | empty |
Compared structures
- 3NGC · Complex of 6-hydroxy-L-nicotine oxidase with intermediate methylmyosmine product formed… · the same entry in another collection · chain X against X, 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 Q93NH4
- Elsewhere: RCSB PDB 3NGC · PDBe 3NGC · UniProt Q93NH4
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