Research workbench
Structure of L-lysine oxidase in complex with L-lysine
Analyse Structure of L-lysine oxidase in complex with L-lysine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C3H
- Type
- protein
- Length
- 1,010 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Hypocrea rufa
- Molecule
- L-lysine oxidase
- EC
- 1.4.3.14
- UniProt
- A0A0J9X1X3
- Ligands
- FAD, LYS
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · resolution 1.7 · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lysine oxidase (EC 1.4.3.14) | protein | 505 | 38% helix, 20% strand | A0A0J9X1X3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- LYS · Lysine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.86 | 0.94 | 69 | FAD, LYS |
| 2 | 627 | 0.85 | 0.89 | 107 | FAD, LYS, GOL |
| 3 | 219 | 0.82 | 0.96 | 41 | empty |
| 4 | 162 | 0.74 | 0.92 | 34 | empty |
| 5 | 160 | 0.74 | 0.92 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 3066 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 7C3H · Structure of L-lysine oxidase in complex with L-lysine · 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 7C3H · PDBe 7C3H · UniProt A0A0J9X1X3
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