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

Dehaloperoxidase B in complex with substrate 4-methyl-cresol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 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: N0D.2 22 PLIP interactions: 22 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.62, A:M.63, A:L.83, A:Q.88, A:L.92, A:N.96, A:F.97, A:F.97, A:L.100, A:L.127 Hydrogen bonds: A:D.54 Water bridges: A:K.58 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89

1 x N0D: 2,4-dimethylphenol(Non-covalent)

N0D.2: 8 residues within 4Å: Chain A: F.21, F.35, H.55, T.56, V.59, F.60, L.100 Ligands: HEM.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:F.35, A:H.55, A:T.56, A:V.59, A:F.60, A:L.100 Water bridges: 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:T.8 Water bridges: A:D.116 EDO.4: 1 residues within 4Å: Chain A: E.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.45 EDO.5: 1 residues within 4Å: Chain A: K.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.99, A:K.99 EDO.6: 8 residues within 4Å: Chain A: L.22, L.25, N.26, K.32, K.41, S.42, D.43, L.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.43 Water bridges: A:K.41

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

SO4.7: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.2, A:K.3, A:D.116 Water bridges: A:S.119 SO4.8: 3 residues within 4Å: Chain A: K.32, V.39, G.40 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.40 Water bridges: A:K.32, A:K.32, A:K.32, A:K.41, 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

2019-09-25

Peptides

Dehaloperoxidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dehaloperoxidase B

Related Entries With Identical Sequence