SMTL ID : 4lj3.1

Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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: 24 residues within 4Å: Chain A: Q.44, E.58, L.60, V.61, R.62, P.73, D.74, I.77, I.86, L.93, N.117, D.179, D.180, K.203, E.236, G.237, V.238, E.239, G.257, Y.258, P.263 Ligands: CA.2, CA.3, IMD.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:Q.44, A:V.61, A:R.62, A:E.81, A:E.81, A:N.117, A:N.117, A:K.203, A:K.203, A:Q.207, A:G.237, A:Y.258 Water bridges: A:S.119, A:D.179, A:E.236, A:E.236 Salt bridges: A:R.62, A:E.239 pi-Stacking: A:Y.258 pi-Cation interactions: A:Y.258 C2E.6: 26 residues within 4Å: Chain B: Q.44, E.58, L.60, V.61, R.62, P.73, D.74, I.77, E.81, I.86, L.93, N.117, D.179, D.180, K.203, Q.207, E.236, G.237, V.238, E.239, G.257, Y.258, P.263 Ligands: CA.7, CA.8, IMD.9 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.44, B:V.61, B:R.62, B:N.117, B:N.117, B:N.117, B:D.179, B:K.203, B:K.203, B:Q.207, B:G.237, B:Y.258 Water bridges: B:S.119, B:T.151 Salt bridges: B:R.62, B:E.81, B:E.239 pi-Stacking: B:Y.258 pi-Cation interactions: B:Y.258

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.58, N.117, E.149, D.179 Ligands: C2E.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.58, A:E.149, A:D.179, H2O.1, C2E.1 CA.3: 3 residues within 4Å: Chain A: D.180, E.236 Ligands: C2E.1 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.180, A:E.236, H2O.1, H2O.4, C2E.1 CA.7: 5 residues within 4Å: Chain B: E.58, N.117, E.149, D.179 Ligands: C2E.6 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:E.58, B:E.149, B:D.179, C2E.6, H2O.10 CA.8: 4 residues within 4Å: Chain B: D.180, D.202, E.236 Ligands: C2E.6 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.180, B:D.202, C2E.6, H2O.10, H2O.12

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 7 residues within 4Å: Chain A: N.117, V.118, S.119, E.149, T.151, D.179 Ligands: C2E.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.118 IMD.9: 7 residues within 4Å: Chain B: N.117, V.118, S.119, E.149, T.151, D.179 Ligands: C2E.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.118, B:D.179

2 x HB0: trans-4-(hydroxymethyl)cyclohexanol(Non-covalent)

HB0.5: 12 residues within 4Å: Chain A: V.46, T.55, G.56, C.57, H.113, V.147, E.149, A.177, F.198, K.200, V.234, F.254 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.46, A:H.113, A:F.198, A:F.198, A:V.234 Hydrogen bonds: A:T.55, A:T.55 HB0.10: 12 residues within 4Å: Chain B: V.46, T.55, G.56, C.57, H.113, V.147, E.149, A.177, F.198, K.200, V.234, F.254 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.46, B:H.113, B:V.147, B:F.198, B:F.198, B:V.234 Hydrogen bonds: B:T.55, B:T.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sundriyal, A. et al., Inherent Regulation of EAL Domain-catalyzed Hydrolysis of Second Messenger Cyclic di-GMP. J.Biol.Chem. (2014)

Release Date

2014-01-29

Peptides

Cyclic di-GMP phosphodiesterase YahA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclic di-GMP phosphodiesterase YahA

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