MolNFT v1 · #179842 · protein
NICA2 variant N462V in complex with (S)-nicotine
7KHO · Amine oxidase: “NICA2 variant N462V in complex with (S)-nicotine”. X-ray diffraction, 2 ligands (NCT, FAD), 16 pockets (best druggability 0.87). MolNFT v1 #179842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KHO
- Type
- protein
- Length
- 1,701 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine oxidase
- UniProt
- F8G0P2
- Ligands
- NCT, FAD
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Amine oxidase | protein | 432 | 36% helix, 25% strand | F8G0P2 |
| D | Amine oxidase | protein | 405 | 35% helix, 21% strand | F8G0P2 |
Ligands and binding sites
- NCT · (S)-3-(1-methylpyrrolidin-2-yl)pyridine · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.87 | 0.94 | 61 | NCT, FAD |
| 2 | 692 | 0.87 | 0.91 | 78 | NCT, FAD |
| 3 | 472 | 0.87 | 0.94 | 64 | NCT, FAD |
| 4 | 482 | 0.87 | 0.93 | 60 | NCT, FAD |
| 5 | 1008 | 0.80 | 0.82 | 103 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1599 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 794 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 694 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 60 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7KHO · NicA2 variant N462V in complex with (S)-nicotine · 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 F8G0P2
- Elsewhere: RCSB PDB 7KHO · PDBe 7KHO · UniProt F8G0P2
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