SMTL ID : 7sjg.1 (1 other biounit)

Structure of Dehaloperoxidase B in Complex with Thymoquinone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 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, 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.127 Ligands: 9J9.5 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:V.59, 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 Metal complexes: A:H.89

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.10, E.65, D.68, R.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.10, A:R.10, A:R.69 GOL.3: 6 residues within 4Å: Chain A: Q.4, D.5, T.8, Q.113, S.114, F.115 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.4, A:D.5, A:Q.113, A:S.114 GOL.4: 5 residues within 4Å: Chain A: K.3, I.6, A.7, R.10, D.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.3, A:A.7, A:R.10, A:R.10

3 x 9J9: (6R)-4-hydroxy-6-methyl-3-(propan-2-yl)cyclohexa-2,4-dien-1-one(Covalent)(Non-covalent)

9J9.5: 7 residues within 4Å: Chain A: F.21, F.35, Y.38, H.55, T.56, V.59 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:Y.38, A:H.55, A:T.56, A:V.59 9J9.7: 5 residues within 4Å: Chain A: D.116, Q.118, S.119 Ligands: 9IX.6, SO4.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.119 Water bridges: A:Q.118 9J9.8: 4 residues within 4Å: Chain A: P.29, D.30, K.32, R.33 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.29, A:D.30

1 x 9IX: 2-methyl-5-(propan-2-yl)benzene-1,4-diol(Covalent)

9IX.6: 7 residues within 4Å: Chain A: F.2, D.72, C.73, S.119, R.122 Ligands: 9J9.7, SO4.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.2

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

SO4.9: 5 residues within 4Å: Chain A: G.1, F.2, K.3 Ligands: 9IX.6, 9J9.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.1, A:F.2, A:K.3 Water bridges: A:Q.4, A:S.119 SO4.10: 3 residues within 4Å: Chain A: K.32, V.39, G.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.40 Salt bridges: A:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2022-11-23

Peptides

Dehaloperoxidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dehaloperoxidase B

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