SMTL ID : 8vzr.1 (1 other biounit)

Crystal structure of dehaloperoxidase A in complex with substrate 4-bromo-o-cresol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 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, Y.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: MWJ.2, OXY.6 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:V.59, A:L.62, A:L.83, A:Q.88, A:L.92, A:L.92, A:F.97, A:L.127 Salt bridges: A:K.58 pi-Cation interactions: A:H.55 Metal complexes: A:H.89

1 x MWJ: 4-bromo-2-methylphenol(Covalent)

MWJ.2: 9 residues within 4Å: Chain A: F.21, F.35, Y.38, F.52, H.55, T.56, V.59 Ligands: HEM.1, OXY.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.21, A:H.55, A:V.59 Hydrogen bonds: A:Y.38, A:T.56 pi-Stacking: A:F.35

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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.4, A:D.5, A:D.5, A:Q.113, A:S.114

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: L.62, E.65, R.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.69, A:R.69

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 3 residues within 4Å: Chain A: G.95, E.98, K.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.99, A:K.99 Water bridges: A:G.95, A:E.98

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.6: 5 residues within 4Å: Chain A: F.35, H.55, V.59 Ligands: HEM.1, MWJ.2 No protein-ligand interaction detected (PLIP)

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

SO4.7: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.2, A:K.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aktar, M.S. et al., Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B. Biochemistry (2024)

Release Date

2024-07-17

Peptides

Dehaloperoxidase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dehaloperoxidase A

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