SMTL ID : 6ong.1 (1 other biounit)

Dehaloperoxidate B in complex with substrate 4-F-cresol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: F.24, E.31, N.34, F.35, D.54, 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.100, L.127 Ligands: MWM.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:V.59, A:L.62, A:L.62, A:M.63, A:L.83, A:L.92, A:N.96, A:F.97, A:F.97, A:L.100, A:L.127 Hydrogen bonds: A:D.54 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89

1 x MWM: 4-fluoro-2-methylphenol(Non-covalent)

MWM.2: 7 residues within 4Å: Chain A: F.21, F.35, H.55, T.56, V.59, L.100 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.35, A:F.35, A:V.59, A:V.59 Water bridges: A:H.55 pi-Stacking: A:F.21

1 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.4, A:T.8 Water bridges: A:D.116

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.1, A:F.2, A:K.3, A:D.116 Water bridges: A:Q.4, A:S.119, A:S.119, A:S.119 SO4.5: 3 residues within 4Å: Chain A: K.32, V.39, G.40 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.40 Water bridges: A:K.41, A:K.41 Salt bridges: A:K.32

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
A

Dehaloperoxidase B

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