SMTL ID : 6ttr.1

Crystal Structure of the coiled coil and GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: I.88, D.89, H.90, K.202, R.206 Chain B: K.92 Ligands: C2E.4 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.88, A:H.90, A:H.90 Salt bridges: A:K.202, A:R.206, B:K.92 PO4.5: 6 residues within 4Å: Chain B: D.87, I.88, D.89, H.90, K.202, R.206 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.90, B:F.91 Salt bridges: B:K.202, B:R.206

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.2: 10 residues within 4Å: Chain A: Q.105, R.108, Y.109, S.112, R.116, R.158, L.160, K.161, R.163 Ligands: C2E.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.105, A:Q.105, A:S.112, A:S.112, A:R.158, A:R.158, A:K.161, A:R.163, A:R.163 Salt bridges: A:R.108, A:R.116, A:R.163 pi-Cation interactions: A:R.163 C2E.3: 3 residues within 4Å: Chain A: R.158, R.163 Ligands: C2E.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.158, A:R.163, A:R.163 C2E.4: 22 residues within 4Å: Chain A: L.54, R.60, F.91, N.95, H.100, G.103, D.104, I.107, R.126, G.129, A.130 Chain B: L.54, F.91, K.92, N.95, H.100, G.103, D.104, I.107, R.126, G.129 Ligands: PO4.1 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:N.95, A:N.95, A:N.95, A:R.126, A:R.126, A:A.130, B:N.95, B:N.95, B:N.95, B:R.126, B:G.129, B:A.130 Salt bridges: A:D.104, B:D.104 pi-Cation interactions: B:H.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holzschuh, F. et al., Crystal structure of the coiled coil and GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP. To Be Published

Release Date

2021-01-13

Peptides

GGDEF diguanylate cyclase DgcB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GGDEF diguanylate cyclase DgcB