SMTL ID : 6zxb.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

GH3.1: 23 residues within 4Å: Chain A: D.169, I.170, D.171, K.172, F.173, K.174, N.177, H.182, G.185, D.186, I.189, R.208, G.211, E.212, K.284, R.288 Chain B: Y.140, Y.144, R.148, Q.151, E.152, R.155 Ligands: MG.4 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:Y.140, B:R.148, B:E.152, A:K.172, A:F.173, A:K.174, A:N.177, A:N.177, A:R.208 pi-Cation interactions: B:R.148, B:R.148 Water bridges: A:N.175 Salt bridges: A:D.186, A:K.284, A:R.288 GH3.10: 18 residues within 4Å: Chain B: D.169, I.170, D.171, K.172, F.173, K.174, N.177, H.182, G.185, D.186, I.189, R.208, G.211, E.212, K.284, R.288 Ligands: MG.12, MG.13 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.172, B:F.173, B:K.174, B:N.177, B:N.177, B:R.208 Salt bridges: B:D.186, B:K.284, B:R.288

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.7, D.8, S.9, D.51, E.53 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.7, A:D.8, A:D.51 MG.3: 4 residues within 4Å: Chain A: D.169, E.212, E.213 Ligands: MG.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.169, A:E.212, A:E.213, H2O.1, H2O.1 MG.4: 6 residues within 4Å: Chain A: D.169, I.170, E.212, K.284 Ligands: GH3.1, MG.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.169, A:I.170, A:E.212, A:E.212 MG.11: 4 residues within 4Å: Chain B: E.7, D.8, D.51, E.53 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.7, B:D.8, B:D.51 MG.12: 5 residues within 4Å: Chain B: D.169, E.212, E.213 Ligands: GH3.10, MG.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.169, B:E.212, B:E.213 MG.13: 6 residues within 4Å: Chain B: D.169, I.170, E.212, K.284 Ligands: GH3.10, MG.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.169, B:I.170, B:E.212

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: R.228, R.232 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.228, A:R.232 SO4.6: 3 residues within 4Å: Chain A: R.155, R.158, H.159 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.158, A:H.159 SO4.7: 1 residues within 4Å: Chain A: R.288 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.172, A:R.288 SO4.8: 2 residues within 4Å: Chain A: H.194, K.197 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.194, A:K.197 SO4.14: 2 residues within 4Å: Chain B: D.160, S.264 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.160

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 3 residues within 4Å: Chain A: I.249, F.250, H.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.251, A:H.251 Water bridges: A:Y.180 EDO.15: 3 residues within 4Å: Chain B: Q.191, L.240, E.241 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.241

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