SMTL ID : 8yk5.1

Structure of glycerophosphoethanolamine ethanolaminephosphodiesterase from Streptomyces sanglieri

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.15, N.16, T.139, D.341, E.342 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.15, A:T.139, A:D.341, A:D.341 CA.3: 6 residues within 4Å: Chain B: E.15, N.16, T.139, D.341, E.342 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.15, B:T.139, B:D.341, B:D.341, B:E.342

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: E.15, N.16, H.81, S.138, T.139, N.163, Y.166, H.304, E.342 Ligands: CA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.16, A:N.16, A:T.139, A:T.139, A:N.163, A:Y.166, A:E.342 GOL.4: 10 residues within 4Å: Chain A: R.436 Chain B: E.15, N.16, H.81, S.138, T.139, N.163, H.304, E.342 Ligands: CA.3 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.436, B:N.16, B:N.16, B:T.139, B:T.139, B:N.163, B:N.163, B:H.304 Water bridges: A:E.439

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murayama, K. et al., Structure of a phosphodiesterase from Streptomyces sanglieri with a novel C-terminal domain. Biochem.Biophys.Res.Commun. (2024)

Release Date

2024-04-03

Peptides

phospholipase C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

phospholipase C