SMTL ID : 6zxm.2 (2 other biounits)

Diguanylate cyclase DgcR in complex with c-di-GMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

4 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: 10 residues within 4Å: Chain A: F.225, R.226, D.229, F.243, T.246, D.250, R.253, I.254 Chain B: R.183 Ligands: C2E.2 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.226, A:R.226, A:T.246, A:T.246, A:R.253, B:R.183, B:R.183 Salt bridges: A:R.226, A:D.229, A:R.253 pi-Cation interactions: A:R.226, A:R.226 C2E.2: 5 residues within 4Å: Chain A: F.225, R.226, K.227 Chain B: R.183 Ligands: C2E.1 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.183, B:R.183, A:R.226, A:K.227 Salt bridges: A:K.227 C2E.4: 11 residues within 4Å: Chain A: R.183 Chain B: S.224, F.225, R.226, D.229, F.243, T.246, D.250, R.253, I.254 Ligands: C2E.5 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.226, B:T.246, B:R.253, A:R.183, A:R.183 Salt bridges: B:R.226, B:D.229, B:R.253 pi-Cation interactions: B:R.226 C2E.5: 7 residues within 4Å: Chain A: Q.179, R.183 Chain B: S.224, F.225, R.226, K.227 Ligands: C2E.4 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.226, B:K.227, B:K.227, A:R.183, A:R.183 Salt bridges: B:K.227, A:R.183

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.32, D.33, D.76, E.78 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.32, A:D.33, A:D.76 MG.6: 4 residues within 4Å: Chain B: E.32, D.33, D.76, E.78 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.32, B:D.33, B:D.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teixeira, R.D. et al., Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase. Nat Commun (2021)

Release Date

2021-03-31

Peptides

Putative GGDEF/response regulator receiver domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Putative GGDEF/response regulator receiver domain protein

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