SMTL ID : 6zxc.1 (1 other biounit)

Diguanylate cyclase DgcR (I-site mutant) in activated state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.32, D.33, D.76, E.78, K.128 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.32, A:D.33, A:E.78 MG.3: 4 residues within 4Å: Chain A: D.194, E.237, E.238 Ligands: GH3.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.194, A:E.237, A:E.238 MG.4: 4 residues within 4Å: Chain A: D.194, I.195, E.237 Ligands: GH3.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.194, A:I.195, A:E.237, A:E.237 MG.5: 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:D.33, B:D.33, B:E.78 MG.7: 4 residues within 4Å: Chain B: D.194, E.237, E.238 Ligands: GH3.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.194, B:E.237, B:E.238 MG.8: 4 residues within 4Å: Chain B: D.194, I.195, E.237 Ligands: GH3.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.194, B:I.195, B:E.237, B:E.237

2 x GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GH3.2: 18 residues within 4Å: Chain A: D.194, I.195, D.196, K.197, F.198, K.199, N.202, H.207, G.210, D.211, I.214, R.233, G.236, E.237, K.309, R.313 Ligands: MG.3, MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.197, A:F.198, A:K.199, A:N.202, A:N.202, A:R.233 Water bridges: A:N.200 Salt bridges: A:K.197, A:D.211, A:K.309, A:R.313 pi-Cation interactions: A:H.207 GH3.6: 19 residues within 4Å: Chain B: D.194, I.195, D.196, K.197, F.198, K.199, N.202, H.207, G.210, D.211, I.214, R.233, G.236, E.237, E.238, K.309, R.313 Ligands: MG.7, MG.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.197, B:F.198, B:K.199, B:N.202, B:N.202, B:R.233 Salt bridges: B:D.211, B:K.309, B:R.313 pi-Cation interactions: B:H.207

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
A

B
B

Putative GGDEF/response regulator receiver domain protein

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