SMTL ID : 6oo1.1 (1 other biounit)

Dehaloperoxidase B in complex with substrate o-cresol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 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.100, L.127 Ligands: JZ0.5 18 PLIP interactions: 18 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:Q.88, A:L.92, A:N.96, A:F.97, A:F.97, A:L.127 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89

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

EDO.2: 4 residues within 4Å: Chain A: Q.4, D.5, T.8, S.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.8 Water bridges: A:D.116 EDO.3: 4 residues within 4Å: Chain A: R.10, E.65, D.68, R.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.10, A:R.10, A:D.68, A:D.68 EDO.4: 3 residues within 4Å: Chain A: T.93, T.94, G.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.93, A:G.95, A:K.99, A:K.99 Water bridges: A:E.98 EDO.6: 4 residues within 4Å: Chain A: D.19, L.22, D.43, K.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.19, A:D.43 EDO.7: 6 residues within 4Å: Chain A: E.98, F.101, V.102, D.121, G.124, K.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.98, A:D.121, A:K.125

1 x JZ0: o-cresol(Non-covalent)

JZ0.5: 7 residues within 4Å: Chain A: F.21, F.35, Y.38, H.55, T.56, V.59 Ligands: HEM.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:F.21, A:F.21, A:F.35, A:Y.38, A:V.59 Hydrogen bonds: A:Y.38, A:Y.38 pi-Stacking: A:F.35

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

SO4.8: 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 SO4.9: 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.32, A:K.32 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

2020-07-22

Peptides

Dehaloperoxidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dehaloperoxidase B

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