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Ancestral L-lys oxidase K387A variant (L-lys binding form)

Analyse Ancestral L-lys oxidase K387A variant (L-lys binding form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EII
Type: protein
Length: 1,170 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FAD dependent L-lys oxidase
Ligands: FAD, LYS
Pockets: 14 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	FAD dependent L-lys oxidase	protein	586	31% helix, 21% strand	—
B	FAD dependent L-lys oxidase	protein	584	31% helix, 22% strand	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
LYS · Lysine · ligand · chains B

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	930	0.89	0.92	144	LYS, FAD
2	1096	0.86	0.86	135	FAD
3	179	0.70	0.88	27	empty
4	135	0.51	0.79	20	empty
5	77	0.49	0.83	21	empty

Interfaces

1 interface between chains.

A–B · 1861 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

7EII · Ancestral L-Lys oxidase K387A variant (L-Lys binding form) · 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 7EII · PDBe 7EII

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