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

Crystal structure of Dehaloperoxidase A in complex with substrate 2,4-dibromophenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 18 residues within 4Å: Chain A: F.24, E.31, Y.34, F.35, H.55, K.58, V.59, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.100, L.127 Ligands: Y8I.2 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, 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:N.96, A:F.97, A:L.100, A:L.127 Salt bridges: A:K.36, A:H.55, A:K.58 pi-Stacking: A:H.55 Metal complexes: A:H.89, H2O.1

1 x Y8I: 2,4-bis(bromanyl)phenol(Covalent)

Y8I.2: 9 residues within 4Å: Chain A: A.17, 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:F.21, A:T.56, A:V.59, A:F.60, A:L.100 pi-Stacking: A:F.21

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

PEG.3: 6 residues within 4Å: Chain A: E.31, R.33, Y.34, G.95, N.96, K.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.34, A:G.95, A:N.96 Water bridges: A:G.95 PEG.4: 6 residues within 4Å: Chain A: E.98, V.102, D.121, G.124, K.125, V.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.98, A:E.98, A:K.125 Water bridges: A:K.125, A:K.125

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

SO4.5: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.2, A:K.3, A:D.116 Water bridges: A:G.1, A:Q.4, A:S.119, A:S.119 SO4.6: 3 residues within 4Å: Chain A: T.15, D.19, K.47 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.19 Water bridges: A:K.47, A:K.47, A:K.47 Salt bridges: A:K.47

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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