SMTL ID : 6ih7.1

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 3',3'-cGAMP bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x 4BW: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one(Non-covalent)

4BW.1: 23 residues within 4Å: Chain A: Q.31, E.45, A.46, L.47, V.48, R.49, A.56, I.60, C.75, N.95, D.158, D.159, M.182, R.186, E.215, G.216, V.217, E.218, G.236, Y.237, P.242 Ligands: CA.2, CA.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.31, A:V.48, A:R.49, A:N.95, A:R.186, A:G.216, A:Y.237, A:Y.237, A:Y.237 Water bridges: A:A.56, A:A.56 Salt bridges: A:R.49, A:E.218 pi-Stacking: A:Y.237, A:Y.237 pi-Cation interactions: A:Y.237 4BW.4: 24 residues within 4Å: Chain B: M.28, Q.31, E.45, A.46, L.47, V.48, R.49, A.56, I.60, N.95, L.97, D.158, D.159, M.182, R.186, E.215, G.216, V.217, E.218, G.236, Y.237, P.242 Ligands: CA.5, CA.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.31, B:A.46, B:V.48, B:R.49, B:R.186, B:E.218, B:Y.237 Salt bridges: B:R.49, B:E.218 pi-Stacking: B:Y.237

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.45, N.95, E.128, D.158 Ligands: 4BW.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.45, A:E.128, A:D.158, H2O.1 CA.3: 4 residues within 4Å: Chain A: D.158, D.159, E.215 Ligands: 4BW.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.158, A:D.159, A:E.215, A:E.215 CA.5: 5 residues within 4Å: Chain B: E.45, N.95, E.128, D.158 Ligands: 4BW.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.45, B:E.128, B:D.158 CA.6: 4 residues within 4Å: Chain B: D.158, D.159, E.215 Ligands: 4BW.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.158, B:D.159, B:E.215, B:E.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yadav, M. et al., Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication. Biochem.J. (2019)

Release Date

2019-10-02

Peptides

cyclic di nucleotide phoshodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

cyclic di nucleotide phoshodiesterase

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