SMTL ID : 8vkc.2 (1 other biounit)

Crystal structure of dehaloperoxidase A in complex with substrate 4-nitrophenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 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, 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: NPO.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.24, A:Y.34, A:F.35, A:V.59, A:L.62, A:L.83, A:Q.88, A:L.92, A:L.92, A:N.96, A:F.97, A:L.100, A:L.127 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89

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

NPO.2: 8 residues within 4Å: Chain A: F.21, F.35, H.55, T.56, V.59, F.60, L.100 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.56, A:V.59, A:V.59 Hydrogen bonds: A:H.55 pi-Stacking: A:F.21, A:F.35

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

SO4.3: 3 residues within 4Å: Chain A: V.39, G.40, K.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.40, A:K.41, A:K.41 SO4.4: 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:G.1, A:F.2, A:K.3, A:D.116 Water bridges: A:Q.4 SO4.5: 5 residues within 4Å: Chain A: Y.28, D.30, E.31, R.33, K.99 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.30, A:E.31 Water bridges: A:Y.28, A:D.30, A:E.31 Salt bridges: A:R.33, A:K.99

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
BBB

Dehaloperoxidase A

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