SMTL ID : 3n3t.1

Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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: 22 residues within 4Å: Chain A: Q.45, E.59, L.61, V.62, R.63, M.73, P.74, V.94, N.120, E.152, D.182, D.183, Q.206, E.239, G.240, I.241, E.242, G.260, N.261, P.266 Ligands: MG.2, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.45, A:V.62, A:R.63, A:N.120, A:S.122, A:Q.206, A:Q.206, A:N.261 Water bridges: A:S.91, A:N.120, A:N.120, A:D.182 Salt bridges: A:R.63, A:E.242 C2E.5: 22 residues within 4Å: Chain B: Q.45, E.59, L.61, V.62, R.63, P.74, I.78, I.87, V.94, N.120, D.182, D.183, Q.206, E.239, G.240, I.241, E.242, G.260, N.261, P.266 Ligands: MG.6, MG.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.45, B:V.62, B:N.120, B:N.120, B:Q.206, B:G.240, B:E.242, B:N.261 Water bridges: B:N.120, B:D.183 Salt bridges: B:R.63, B:E.242

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.59, N.120, E.152, D.182 Ligands: C2E.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.59, A:E.152, A:D.182, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.182, D.183, D.205, E.239 Ligands: C2E.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.182, A:D.183, A:E.239, H2O.1 MG.6: 6 residues within 4Å: Chain B: E.59, N.120, E.152, D.182, K.203 Ligands: C2E.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.59, B:E.152, B:D.182, H2O.9 MG.7: 4 residues within 4Å: Chain B: D.182, D.183, E.239 Ligands: C2E.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.182, B:D.183, B:E.239, B:E.239, H2O.9

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

CL.4: 1 residues within 4Å: Chain A: R.145 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tchigvintsev, A. et al., Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases. J.Mol.Biol. (2010)

Release Date

2010-06-16

Peptides

PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE

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