SMTL ID : 6onk.2 (1 other biounit)

Dehaloperoxidase B in complex with substrate 4-Cl-cresol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 19 residues within 4Å: Chain A: F.24, E.31, N.34, F.35, H.55, K.58, V.59, L.62, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.127 Ligands: MZG.2, EDO.4 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:V.59, A:L.62, A:M.63, A:L.83, A:Q.88, A:L.92, A:N.96, A:L.127 Water bridges: A:Q.88 Salt bridges: A:K.58 pi-Cation interactions: A:H.55 Metal complexes: A:H.89, H2O.2

1 x MZG: 4-chloro-2-methylphenol(Non-covalent)

MZG.2: 9 residues within 4Å: Chain A: A.17, F.21, F.35, H.55, T.56, V.59, F.60, L.100 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:T.56, A:V.59, A:V.59, A:L.100 Hydrogen bonds: A:H.55 pi-Stacking: A:F.21

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

EDO.3: 5 residues within 4Å: Chain A: Q.4, D.5, T.8, S.114, F.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.4, A:T.8 EDO.4: 5 residues within 4Å: Chain A: F.35, K.36, N.37, Y.38 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.35, A:N.37 Water bridges: A:N.37 EDO.5: 5 residues within 4Å: Chain A: E.31, T.93, G.95, N.96, K.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.31, A:K.99 EDO.6: 3 residues within 4Å: Chain A: S.111, G.112, Q.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.112, A:Q.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malewschik, T. et al., The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants. Arch.Biochem.Biophys. (2019)

Release Date

2019-09-11

Peptides

Dehaloperoxidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dehaloperoxidase B

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