SMTL ID : 7t9c.2 (1 other biounit)

Crystal structure of dehaloperoxidase B in complex with thymol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: F.24, E.31, 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: IPB.2 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:K.58, A:V.59, 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 Hydrogen bonds: A:Q.88 Salt bridges: A:K.58 pi-Cation interactions: A:H.55, A:H.55 Metal complexes: A:H.89, H2O.1

1 x IPB: 5-METHYL-2-(1-METHYLETHYL)PHENOL(Covalent)

IPB.2: 9 residues within 4Å: Chain A: F.21, F.35, Y.38, K.51, F.52, H.55, T.56, V.59 Ligands: HEM.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:F.35, A:Y.38, A:F.52, A:H.55, A:H.55, A:H.55, A:T.56 Hydrogen bonds: A:Y.38, A:T.56 pi-Cation interactions: A:H.55

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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.4, A:D.5, A:T.8, A:Q.113, A:S.114 Water bridges: A:S.114, A:D.116 GOL.4: 6 residues within 4Å: Chain A: E.98, F.101, V.102, D.121, G.124, K.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.121

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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