SMTL ID : 4lyk.1 (2 other biounits)

Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.58, N.117, E.149, D.179 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.58, A:E.149, A:D.179, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain B: E.58, N.117, E.149, D.179 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, B:E.149, B:D.179, H2O.4, H2O.5

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

HB0.2: 11 residues within 4Å: Chain A: V.46, T.55, G.56, C.57, H.113, V.147, E.149, F.198, K.200, V.234, F.254 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.46, A:H.113, A:V.147, A:F.198, A:F.198, A:V.234 Hydrogen bonds: A:T.55, A:E.149 HB0.6: 11 residues within 4Å: Chain B: V.46, T.55, G.56, C.57, H.113, V.147, E.149, 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

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 9 residues within 4Å: Chain A: F.181, G.182, A.186, T.187, Y.188 Chain B: G.182, A.186, T.187, Y.188 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.186, A:Y.188, B:Y.188 EDO.4: 7 residues within 4Å: Chain A: L.150, T.151, P.155, I.156, L.178, Y.185, Y.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.156, A:Y.185 EDO.7: 8 residues within 4Å: Chain B: L.150, T.151, P.155, I.156, L.178, Y.185, A.186, Y.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.156, B:Y.185

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

Related Entries With Identical Sequence