SMTL ID : 8u0i.1

Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

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: 8 residues within 4Å: Chain A: D.4, N.5, Q.6, R.7, R.11, R.76 Ligands: C2E.2, GOL.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.5, A:N.5, A:Q.6, A:Q.6, A:R.7, A:R.7, A:R.11, A:R.11, A:R.76, A:R.76, A:R.76 Water bridges: A:R.7, A:R.7 Salt bridges: A:R.7 pi-Cation interactions: A:R.76 C2E.2: 19 residues within 4Å: Chain A: Q.6, R.7, Q.8, Y.9, R.11, D.34, L.35, S.36, T.38, G.39, V.40, Y.41, V.75, R.76, G.83, L.84, R.85 Ligands: C2E.1, GOL.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:Q.6, A:R.7, A:R.7, A:Q.8, A:R.11, A:R.11, A:S.36, A:T.38, A:G.39, A:Y.41, A:R.76, A:R.76 Water bridges: A:Y.9, A:Y.9, A:D.34, A:T.38, A:T.38, A:V.75 Salt bridges: A:R.11, A:D.34 pi-Cation interactions: A:R.11

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: I.20, S.21, H.22, F.25, G.26, E.27, L.28, D.46, L.47, L.50, V.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.27, A:D.46 GOL.4: 2 residues within 4Å: Chain A: Q.6 Ligands: C2E.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.6 GOL.5: 1 residues within 4Å: Ligands: C2E.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hammons, N.A. et al., Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa. To Be Published

Release Date

2024-09-04

Peptides

PilZ domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PilZ domain-containing protein