MolNFT v1 · #174693 · protein
Structure of L-lysine oxidase D212A/D315A in complex with L- phenylalanine
7C3J: “Structure of L-lysine oxidase D212A/D315A in complex with L- phenylalanine”. X-ray diffraction, 3 ligands (FAD, PHE, SO4), 10 pockets (best druggability 0.86). MolNFT v1 #174693 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7C3J
- Type
- protein
- Length
- 1,018 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lysine oxidase
- EC
- 1.4.3.14
- UniProt
- A0A0J9X1X3
- Ligands
- FAD, PHE, SO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lysine oxidase (EC 1.4.3.14) | protein | 509 | 39% helix, 20% strand | A0A0J9X1X3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PHE · Phenylalanine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.86 | 0.88 | 111 | FAD, PHE, GOL |
| 2 | 1080 | 0.85 | 0.86 | 115 | FAD, PHE, GOL |
| 3 | 200 | 0.81 | 0.95 | 41 | empty |
| 4 | 137 | 0.73 | 0.93 | 26 | empty |
| 5 | 126 | 0.71 | 0.92 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3022 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 7C3J · Structure of L-lysine oxidase D212A/D315A in complex with L-phenylalanine · 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 A0A0J9X1X3
- Elsewhere: RCSB PDB 7C3J · PDBe 7C3J · UniProt A0A0J9X1X3
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