SMTL ID : 5llw.1

Bacteriophytochrome activated diguanylyl cyclase from Idiomarina species A28L

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(Covalent)

LBV.1: 29 residues within 4Å: Chain A: C.19, I.24, M.168, Y.170, V.180, F.197, S.200, D.201, I.202, P.203, A.206, Y.210, R.216, I.218, R.248, V.250, S.251, L.253, H.254, Y.257, F.261, S.266, S.268, I.280, A.282, H.284, L.466, G.467, P.468 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.24, A:I.24, A:Y.170, A:V.180, A:F.197, A:F.197, A:I.202, A:I.202, A:P.203, A:A.206, A:R.216, A:L.253, A:Y.257, A:I.280 Hydrogen bonds: A:D.201, A:D.201, A:A.249, A:S.251, A:S.266, A:S.268 Salt bridges: A:R.216, A:R.248, A:H.254 pi-Cation interactions: A:H.254 LBV.3: 26 residues within 4Å: Chain B: C.19, I.24, M.168, Y.170, V.180, 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, 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:V.180, B:F.197, B:F.197, B:F.197, B:D.201, B:I.202, B:I.202, B:P.203, B:A.206, B:V.250, B:L.253, B:I.280 Hydrogen bonds: B:D.201, B:D.201, B:D.201, B:D.201, B:Y.210, B:S.251, B:S.266 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: 4 residues within 4Å: Chain A: V.246, R.293, R.296, R.297 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain B: L.107, V.246, R.293, R.296, R.297 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gourinchas, G. et al., Long-range allosteric signaling in red light-regulated diguanylyl cyclases. Sci Adv (2017)

Release Date

2017-03-15

Peptides

Diguanylate cyclase (GGDEF) domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Diguanylate cyclase (GGDEF) domain-containing protein

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