SMTL ID : 7t9d.2 (1 other biounit)

Crystal structure of dehaloperoxidase B in complex with -(-) limonene oxide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 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, Y.38, 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: GHI.5 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.24, A:F.35, A:K.58, A:V.59, A:L.62, A:L.62, A:M.63, A:L.83, A:Q.88, A:Q.88, A:L.92, A:L.92, A:F.97, A:L.100, A:L.127 Salt bridges: A:H.55 pi-Cation interactions: A:H.55, A:H.55 Metal complexes: A:H.89, H2O.2

2 x GHI: (1S,4S,6R)-1-methyl-4-(prop-1-en-2-yl)-7-oxabicyclo[4.1.0]heptane(Non-covalent)(Covalent)

GHI.2: 5 residues within 4Å: Chain A: E.31, T.93, G.95, N.96, K.99 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.99 Water bridges: A:N.96 GHI.5: 7 residues within 4Å: Chain A: F.21, F.35, Y.38, H.55, T.56, V.59 Ligands: HEM.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:F.35, A:F.35, A:H.55, A:H.55, A:H.55, A:T.56, A:V.59

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Q.4, D.5, T.8, Q.113, S.114, F.115 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.4, A:T.8, A:Q.113, A:S.114 Water bridges: A:D.116 GOL.4: 4 residues within 4Å: Chain A: T.82, Q.85, M.86, K.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.85, A:K.87

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

SO4.6: 3 residues within 4Å: Chain A: D.12, T.15, Y.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malewschik, T. et al., The Multifunctional Globin Dehaloperoxidase as a Biocatalyst in the Oxidation of Monoterpenes. To Be Published

Release Date

2023-01-25

Peptides

Dehaloperoxidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dehaloperoxidase B

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