MolNFT v1 · #117691 · protein

Crystal structure of LOV2-ZDK1 - the complex of oat LOV2 and the affibody protein ZDARK1

5EFW · NPH1-1: “Crystal structure of LOV2-ZDK1 - the complex of oat LOV2 and the affibody protein ZDARK1”. X-ray diffraction, 2 ligands (FMN, SO4), 2 pockets (best druggability 0.71). MolNFT v1 #117691 on GenesisL1: 3D structure, binding…

PDB: 5EFW
Type: protein
Length: 245 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NPH1-1; Z-dark, a small protein based on the Z domain affibody
UniProt: O49003
Ligands: FMN, SO4
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NPH1-1	protein	141	34% helix, 28% strand	O49003
B	Z-dark, a small protein based on the Z domain affibody	protein	55	78% helix, 0% strand	—
C	Z-dark, a small protein based on the Z domain affibody	protein	49	73% helix, 0% strand	—

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · chains A
SO4 · Sulfate ion · ion · 6 copies · chains A, C, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	180	0.71	0.88	22	FMN
2	50	0.32	0.77	13	empty

Interfaces

3 interfaces between chains.

A–C · 778 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 746 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 305 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5EFW · Crystal structure of LOV2-Zdk1 - the complex of oat LOV2 and the affibody protein Zdark1 · 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 O49003
Elsewhere: RCSB PDB 5EFW · PDBe 5EFW · UniProt O49003

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