SMTL ID : 6hbz.1

Bdellovibrio bacteriovorus DgcB Full-length

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

2 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: 13 residues within 4Å: Chain A: K.184, L.185, I.186, R.187, S.188, R.218 Chain B: L.185, R.187, D.190, T.211, V.215, R.218 Ligands: C2E.2 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:I.186, A:R.187, A:S.188, B:R.187, B:R.187, B:R.218, B:R.218 Water bridges: A:K.184, B:R.187, B:N.189, B:N.189, B:S.205, B:S.207, B:T.211, B:T.211 Salt bridges: B:R.187, B:D.190 pi-Cation interactions: B:R.187 C2E.2: 16 residues within 4Å: Chain A: L.185, I.186, R.187, D.190, L.204, T.211, E.214, V.215, R.218 Chain B: K.184, L.185, I.186, R.187, S.188, R.218 Ligands: C2E.1 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.187, A:R.187, A:R.218, B:R.187, B:S.188, B:R.218, B:R.218 Water bridges: A:R.187, A:S.207, A:S.207, A:T.211, A:T.211, A:T.211, B:R.218, B:R.218 Salt bridges: A:R.187, A:D.190 pi-Cation interactions: A:R.187

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: P.135, T.251, E.252, W.253 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: S.44, R.45 Chain B: D.25 Ligands: CL.7 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: R.30, S.44, R.45 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: H.157, R.272 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: R.45, S.46 Chain B: D.25, V.27, K.49 Ligands: CL.4 Ligand excluded by PLIP

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

EDO.8: 3 residues within 4Å: Chain B: S.209, T.245, L.247 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.209, B:T.245 EDO.9: 2 residues within 4Å: Chain B: D.171, R.194 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.171, B:R.194, B:G.197 EDO.10: 3 residues within 4Å: Chain B: I.69, G.72, K.90 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.72 EDO.11: 4 residues within 4Å: Chain B: T.122, G.123, I.182, T.183 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meek, R.W. et al., Structural basis for activation of a diguanylate cyclase required for bacterial predation in Bdellovibrio. Nat Commun (2019)

Release Date

2019-08-28

Peptides

GGDEF domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GGDEF domain protein