SMTL ID : 8c05.1

LOV-activated diguanylate cyclase, dark-state structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 19 residues within 4Å: Chain A: T.26, S.28, N.59, C.60, R.61, L.63, Q.64, V.73, I.76, K.77, M.80, L.90, N.92, N.102, L.104, L.106, Y.119, G.121, Q.123 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.106 Hydrogen bonds: A:N.59, A:N.59, A:C.60, A:Q.64, A:Q.64, A:N.92, A:N.92, A:N.102, A:Q.123 Salt bridges: A:R.61, A:K.77 FMN.4: 19 residues within 4Å: Chain B: T.26, S.28, N.59, C.60, R.61, L.63, Q.64, V.73, I.76, K.77, M.80, L.90, N.92, N.102, L.104, L.106, Y.119, G.121, Q.123 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.106 Hydrogen bonds: B:N.59, B:N.59, B:C.60, B:Q.64, B:Q.64, B:N.92, B:N.92, B:N.102, B:Q.123 Salt bridges: B:R.61, B:K.77

2 x DPO: DIPHOSPHATE(Non-covalent)

DPO.2: 10 residues within 4Å: Chain A: D.192, I.193, D.194, Y.195, F.196, K.197, E.236, K.308, K.312 Ligands: MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.195, A:F.196, A:K.197 Salt bridges: A:K.197, A:K.308, A:K.312 DPO.5: 10 residues within 4Å: Chain B: D.192, I.193, D.194, Y.195, F.196, K.197, E.236, K.308, K.312 Ligands: MG.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.195, B:F.196, B:K.197 Salt bridges: B:K.197, B:K.308, B:K.312

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.192, I.193, E.236, K.308 Ligands: DPO.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.192, A:I.193, A:E.236, A:E.236 MG.6: 5 residues within 4Å: Chain B: D.192, I.193, E.236, K.308 Ligands: DPO.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.192, B:I.193, B:E.236, B:E.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vide, U. et al., Illuminating the inner workings of a natural protein switch: Blue-light sensing in LOV-activated diguanylate cyclases. Sci Adv (2023)

Release Date

2023-07-19

Peptides

Sensor domain-containing diguanylate cyclase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Sensor domain-containing diguanylate cyclase