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

Dehaloperoxidase B in complex with substrate 4-Br-cresol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: I.6, A.7, R.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.10 Water bridges: A:A.7 EDO.4: 5 residues within 4Å: Chain A: Q.4, D.5, T.8, S.114, F.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.4, A:T.8 Water bridges: A:D.116 EDO.5: 5 residues within 4Å: Chain A: F.35, K.36, N.37, Y.38 Ligands: HEM.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.35, A:N.37, A:N.37

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

HEM.2: 20 residues within 4Å: Chain A: F.24, E.31, N.34, F.35, K.51, 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: MWJ.3, EDO.5 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:V.59, A:V.59, A:L.62, A:L.83, A:Q.88, A:Q.88, A:L.92, A:N.96, A:F.97, A:F.97, A:L.127 Salt bridges: A:K.51, A:K.51, A:H.55, A:K.58 pi-Stacking: A:H.55 Metal complexes: A:H.89

1 x MWJ: 4-bromo-2-methylphenol(Non-covalent)

MWJ.3: 9 residues within 4Å: Chain A: A.17, F.21, F.35, H.55, T.56, V.59, F.60, L.100 Ligands: HEM.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:T.56, A:V.59, A:V.59, A:L.100, A:L.100 Hydrogen bonds: A:H.55 pi-Stacking: A:F.21

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

2019-09-25

Peptides

Dehaloperoxidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dehaloperoxidase B

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