SMTL ID : 5chq.1 (1 other biounit)

Dehaloperoxidase B in complex with substrate p-nitrophenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 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: NPO.4 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:V.59, A:L.62, A:M.63, A:L.83, A:Q.88, A:N.96, A:F.97, A:L.100, A:L.127 Hydrogen bonds: A:Q.88, A:Q.88 Water bridges: A:K.58 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89

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

SO4.2: 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

1 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.4, A:D.5, A:D.5 Water bridges: A:D.116

1 x NPO: P-NITROPHENOL(Non-covalent)

NPO.4: 9 residues within 4Å: Chain A: F.21, F.35, Y.38, H.55, T.56, V.59, F.60, L.100 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.35, A:T.56, A:V.59, A:V.59 Hydrogen bonds: A:H.55 pi-Stacking: A:F.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCombs, N.L. et al., Nonmicrobial Nitrophenol Degradation via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin from Amphitrite ornata. Biochemistry (2016)

Release Date

2016-04-27

Peptides

Dehaloperoxidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dehaloperoxidase B

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