SMTL ID : 5efw.1

Crystal structure of LOV2-Zdk1 - the complex of oat LOV2 and the affibody protein Zdark1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-2-mer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: V.15, T.17, N.24, N.48, A.49, R.50, L.52, Q.53, V.62, I.65, R.66, I.69, L.79, N.81, N.91, F.93, L.95, F.108, I.109, G.110, Q.112 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.15, A:T.17, A:I.69, A:F.93, A:L.95 Hydrogen bonds: A:N.48, A:A.49, A:Q.53, A:Q.53, A:N.81, A:N.81, A:N.91, A:Q.112 Salt bridges: A:R.50

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: D.100, Q.101 Chain C: R.13 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.13 Hydrogen bonds: A:Q.101 SO4.3: 5 residues within 4Å: Chain A: R.9, I.10, E.11, K.12, N.137 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.11, A:N.137 Water bridges: A:K.12, A:K.12, A:K.12, A:K.12 Salt bridges: A:K.12 SO4.4: 4 residues within 4Å: Chain A: T.73, E.74, P.97, R.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.72, A:E.74 Salt bridges: A:R.99 SO4.5: 1 residues within 4Å: Chain A: R.125 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.125 SO4.6: 3 residues within 4Å: Chain A: E.42 Chain B: N.25, V.26 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.26 Water bridges: B:N.25, A:R.47 SO4.7: 3 residues within 4Å: Chain B: Q.42, N.45 Chain C: K.52 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.42, B:N.45 Salt bridges: C:K.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., LOVTRAP: an optogenetic system for photoinduced protein dissociation. Nat.Methods (2016)

Release Date

2016-07-20

Peptides

NPH1-1: A
Z-dark, a small protein based on the Z domain affibody: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

NPH1-1

Z-dark, a small protein based on the Z domain affibody

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