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Crystal structure of inhibitor-bound in active centre 6-hydroxy-L- nicotine oxidase from arthrobacter nicotinovorans
Analyse Crystal structure of inhibitor-bound in active centre 6-hydroxy-L- nicotine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NN6
- 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
- HNK, FB0, GP7
- Pockets
- 3 · best druggability 0.85
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
- HNK · 5-[(2R)-1-methylpyrrolidin-2-yl]pyridin-2-ol · ligand · chains X
- FB0 · (2R,3S,4S)-5-({[(acetylcarbamoyl)amino]methyl}[(3S,4R)-6-amino-3,4-dimethylhexyl]amino)-2,3,4-trihydroxypentyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) · ligand · chains X
- GP7 · (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate · ligand · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.85 | 0.92 | 67 | HNK, FB0 |
| 2 | 426 | 0.74 | 0.83 | 50 | GP7 |
| 3 | 105 | 0.45 | 0.78 | 18 | empty |
Compared structures
- 3NN6 · Crystal structure of inhibitor-bound in active centre 6-hydroxy-L-nicotine oxidase from… · 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 3NN6 · PDBe 3NN6 · UniProt Q93NH4
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