SMTL ID : 6saw.2 (3 other biounits)

Chromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from Idiomarina species A28L (dimeric Pfr-like state).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x LBV: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid(Non-covalent)(Covalent)

LBV.1: 23 residues within 4Å: Chain A: C.19, D.20, Y.170, M.192, F.197, S.200, D.201, I.202, P.203, A.206, Y.210, R.216, R.248, V.250, S.251, L.253, H.254, Y.257, F.261, S.268, H.284 Chain B: L.188, T.190 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.170, A:I.202, A:A.206, A:L.253, A:H.254, A:Y.257, A:F.261, B:L.188, B:T.190 Hydrogen bonds: A:D.201, A:D.201, A:Y.210, A:Y.210, A:S.268 Salt bridges: A:R.216, A:R.248, A:H.254 LBV.3: 21 residues within 4Å: Chain A: T.190 Chain B: C.19, D.20, I.24, Y.170, M.192, H.195, F.197, D.201, I.202, P.203, A.206, Y.210, R.216, R.248, V.250, L.253, H.254, Y.257, F.261, H.284 20 PLIP interactions: 1 interactions with chain A, 19 interactions with chain B Hydrophobic interactions: A:T.190, B:I.24, B:Y.170, B:I.202, B:A.206, B:H.254, B:Y.257, B:F.261 Hydrogen bonds: B:Y.170, B:Y.170, B:D.201, B:D.201, B:D.201, B:H.254, B:Y.257 Water bridges: B:D.201 Salt bridges: B:R.216, B:R.248, B:H.254, B:H.284

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: R.293, R.296, R.297 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: R.293, R.296, R.297 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buhrke, D. et al., Distinct chromophore-protein environments enable asymmetric activation of a bacteriophytochrome-activated diguanylate cyclase. J.Biol.Chem. (2020)

Release Date

2019-12-11

Peptides

Diguanylate cyclase (GGDEF) domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

Diguanylate cyclase (GGDEF) domain-containing protein

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