SMTL ID : 6et7.1

Activated heterodimer of the bacteriophytochrome regulated diguanylyl cyclase variant - S505V A526V - from Idiomarina species A28L

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 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, M.168, Y.170, H.195, 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, H.284, L.466, P.468, S.471 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.170, A:D.201, A:I.202, A:A.206, A:Y.257, A:F.261, A:P.468 Hydrogen bonds: A:Y.170, A:D.201, A:D.201, A:Y.257, A:S.266, A:S.471 Water bridges: A:H.254, A:H.254 Salt bridges: A:R.216, A:R.248, A:H.254, A:H.284 LBV.3: 27 residues within 4Å: Chain B: C.19, I.24, Y.170, V.180, F.197, S.200, D.201, I.202, P.203, A.206, Y.210, R.216, I.218, R.248, A.249, V.250, S.251, L.253, H.254, Y.257, S.266, S.268, I.280, A.282, H.284, L.466, P.468 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:I.24, B:Y.170, B:Y.170, B:V.180, B:F.197, B:F.197, B:F.197, B:I.202, B:I.202, B:P.203, B:A.206, B:L.253, B:H.254, B:I.280 Hydrogen bonds: B:D.201, B:D.201, B:S.251, B:S.266, B:S.268 Water bridges: B:H.254, B:H.254 Salt bridges: B:R.216, B:R.248, B:H.254 pi-Cation interactions: B:H.254

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

Gourinchas, G. et al., Asymmetric activation mechanism of a homodimeric red light regulated photoreceptor. Elife (2018)

Release Date

2018-06-13

Peptides

Diguanylate cyclase (GGDEF) domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Diguanylate cyclase (GGDEF) domain-containing protein