SMTL ID : 8vkc.1 (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, Y.38, H.55, K.58, V.59, L.62, M.63, L.83, Q.88, H.89, L.92, N.96, F.97, L.100, F.101 Ligands: NPO.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:V.59, A:V.59, A:M.63, A:L.83, A:Q.88, A:L.92, A:L.92, A:F.97, A:F.101 Hydrogen bonds: A:Y.38 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, Y.38, H.55, T.56, V.59, L.100 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:T.56, A:V.59, A:V.59 Hydrogen bonds: A:Y.38 pi-Stacking: A:F.35

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Q.4, D.5, T.8, Q.113, S.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.4, A:D.5, A:D.5 Water bridges: A:S.114

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
AAA

Dehaloperoxidase A

Related Entries With Identical Sequence