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Crystal structure of LOV2 (C450A) domain in complex with ZDK2

Analyse Crystal structure of LOV2 (C450A) domain in complex with ZDK2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DJT
Type: protein
Length: 203 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NPH1-2; Engineered protein, ZDK2 affibody
UniProt: O49004
Ligands: FMN, CU, CL
Pockets: 1 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NPH1-2	protein	144	35% helix, 27% strand	O49004
B	Engineered protein, ZDK2 affibody	protein	59	69% helix, 0% strand	—

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · chains A
CU · Copper (II) ion · metal · chains A
CL · Chloride ion · ion · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	182	0.69	0.87	25	FMN, CL

Interfaces

1 interface between chains.

A–B · 870 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5DJT · Crystal structure of LOV2 (C450A) domain in complex with Zdk2 · 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 O49004
Elsewhere: RCSB PDB 5DJT · PDBe 5DJT · UniProt O49004

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