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

Dehaloperoxidase B in complex with substrate p-nitrocatechol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 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, H.55, K.58, V.59, L.62, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, F.101, L.127 Ligands: 4NC.4, OXY.5 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:K.58, 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.101, A:L.127 Water bridges: A:Q.88 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89

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

SO4.2: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.1, A:F.2, A:K.3 Water bridges: A:Q.4, A:S.119, A:S.119 SO4.3: 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 4NC: 4-NITROCATECHOL(Non-covalent)

4NC.4: 10 residues within 4Å: Chain A: F.21, F.35, Y.38, F.52, H.55, T.56, V.59, F.60 Ligands: HEM.1, OXY.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.59 Hydrogen bonds: A:Y.38, A:Y.38, A:Y.38, A:T.56 pi-Stacking: A:F.21, A:F.35

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.5: 4 residues within 4Å: Chain A: F.35, V.59 Ligands: HEM.1, 4NC.4 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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:Q.4, A:D.5, A:S.114, A:S.114 GOL.7: 2 residues within 4Å: Chain A: E.65, R.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.65, A:R.69 Water bridges: A:R.69

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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