5EFW: NPH1-1

Crystal structure of LOV2-Zdk1 - the complex of oat LOV2 and the affibody protein Zdark1. Determined by X-ray diffraction at 2.1 Å resolution. Released 20 Jul 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Avena sativa, Staphylococcus aureus
Chains: 3
Atoms: 2,114
Mol. weight: 30.8 kDa
Ligands: FMN
Released: 20 Jul 2016

Explore 5EFW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EFW contains 13 α-helices and 5 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	414-418	5	1
β-strand	427-430	4	1
α-helix	432-438	7
α-helix	442-445	4
α-helix	450-453	4
α-helix	460-471	12
β-strand	476-483	8	1
β-strand	489-500	12	1
β-strand	506-516	11	1
α-helix	522-542	21

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	6-18	13
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-54	14

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-54	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NPH1-1	A	protein	145	Avena sativa	O49003 (AlphaFold model)
Z-dark, a small protein based on the Z domain affibody	B, C	protein	60	Staphylococcus aureus

Sequence of entity 1 (A), FASTA

>5EFW_1 NPH1-1 (chains A)
GSLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRA
TVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVR
DAAEREGVMLIKKTAENIDEAAKEL

Sequence of entity 2 (B, C), FASTA

>5EFW_2 Z-dark, a small protein based on the Z domain affibody (chains B, C)
GSVDNKFNKEKTRAGAEIHSLPNLNVEQKFAFIVSLFDDPSQSANLLAEAKKLNDAQAPK

Ligands and cofactors

ID	Name	Formula	Copies
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

LOVTRAP: an optogenetic system for photoinduced protein dissociation. Wang, H., Vilela, M., Winkler, A. et al. Nat Methods (2016) 13:755-758. DOI 10.1038/nmeth.3926 · PubMed

Other PDB entries of the same protein (UniProt O49003 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7PGZ 0.9 Å, Structure of dark-adapted AsLOV2 Q513L
7PH0 0.98 Å, Structure of light-adapted AsLOV2 Q513L
7PGX 1.0 Å, Structure of dark-adapted AsLOV2 wild type
7PGY 1.09 Å, Structure of light-adapted AsLOV2 wild type
2V0U 1.4 Å, n- and c-terminal helices of oat lov2 (404-546) are involved in light-induced signal…
2V1B 1.55 Å, N- and C-terminal helices of oat LOV2 (404-546) are involved in light-induced signal…
2WKQ 1.6 Å, Structure of a photoactivatable Rac1 containing the Lov2 C450A Mutant
2V1A 1.65 Å, N- and C-terminal helices of oat LOV2 (404-546) are involved in light-induced signal…
2V0W 1.7 Å, N- and C-terminal helices of oat LOV2 (404-546) are involved in light- induced signal…
6NTP 1.89 Å, PTP1B Domain of PTP1B-LOV2 Chimera
2WKP 1.9 Å, Structure of a photoactivatable Rac1 containing Lov2 Wildtype
4WF0 1.95 Å, Crystal Structure of iLID - an Improved Light-Inducible Dimer

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