MolNFT v1 · #84034 · protein

Structure of L-lysine oxidase

3X0V: “Structure of L-lysine oxidase”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.85). MolNFT v1 #84034 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3X0V
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
Ligands: FAD
Pockets: 8 · best druggability 0.85

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	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	805	0.85	0.88	95	FAD, EPE
2	809	0.85	0.88	98	FAD, EPE
3	733	0.80	0.84	81	empty
4	298	0.56	0.76	42	empty
5	233	0.52	0.76	44	empty

Interfaces

1 interface between chains.

A–B · 521 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3X0V · Structure of L-lysine oxidase · 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
Elsewhere: RCSB PDB 3X0V · PDBe 3X0V

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