SMTL ID : 5y6f.1

Crystal structure of YcgR in complex with c-di-GMP from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: G.79, R.114, Y.116, F.117, R.118 Ligands: C2E.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.118 Water bridges: A:A.80 Salt bridges: A:R.114

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.2: 18 residues within 4Å: Chain A: R.113, R.114, R.115, Y.116, R.118, D.145, L.146, S.147, G.149, G.150, M.151, G.152, I.189, R.208, S.210, F.211, R.212 Ligands: C2E.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.113, A:R.114, A:R.115, A:Y.116, A:R.118, A:R.118, A:S.147, A:S.147, A:G.149, A:G.152, A:R.208 Water bridges: A:R.113, A:D.145, A:R.208 Salt bridges: A:R.115, A:R.118, A:D.145, A:R.212 pi-Cation interactions: A:R.113, A:R.118, A:R.118 C2E.3: 16 residues within 4Å: Chain A: E.76, G.79, A.80, K.81, V.111, Q.112, R.113, R.114, R.118, I.189, S.190, S.192, R.208, S.210 Ligands: SO4.1, C2E.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.79, A:G.79, A:R.113, A:R.113, A:R.114, A:R.114, A:R.118, A:R.118, A:S.190, A:S.192, A:S.210 Water bridges: A:A.80, A:A.80, A:A.80, A:A.80, A:K.81, A:K.81, A:R.208 Salt bridges: A:K.81, A:R.114, A:R.208 pi-Cation interactions: A:R.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hou, Y.J. et al., Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility inEscherichia coli. J.Biol.Chem. (2020)

Release Date

2018-07-18

Peptides

Flagellar brake protein YcgR: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Flagellar brake protein YcgR