SMTL ID : 3tvk.1

Diguanylate cyclase domain of DgcZ

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x C2E: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)(Non-covalent)

C2E.1: 11 residues within 4Å: Chain A: L.9, F.44, K.45, N.48, H.53, G.56, D.57, L.60, R.79, G.82, E.83 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.48, A:H.53, A:R.79, A:G.82, A:E.83 Water bridges: A:N.48, A:E.83 Salt bridges: A:D.57 C2E.2: 8 residues within 4Å: Chain A: S.69, W.70, T.71, R.72, D.73, R.103 Ligands: C2E.3, MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.72, A:D.73, A:R.103 Water bridges: A:R.103, A:R.103 pi-Cation interactions: A:R.103, A:R.103 C2E.3: 10 residues within 4Å: Chain A: R.72, Y.74, E.75, V.89, K.90, E.96, R.99, A.100, R.103 Ligands: C2E.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.74, A:K.90, A:R.103 Water bridges: A:R.72, A:R.72, A:E.75, A:E.96, A:E.96, A:E.96 Salt bridges: A:R.72, A:E.75, A:R.99 pi-Cation interactions: A:R.72

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: D.73 Ligands: C2E.2 6 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: A:D.73, C2E.2, H2O.3, H2O.4, H2O.4, H2O.5

1 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.5: 2 residues within 4Å: Chain A: R.43, G.155 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zahringer, F. et al., Structure and signaling mechanism of a zinc-sensory diguanylate cyclase. Structure (2013)

Release Date

2012-10-03

Peptides

Diguanylate cyclase DgcZ: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diguanylate cyclase DgcZ