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

Dehaloperoxidase B in complex with 2,2'-Biphenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 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, 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: 5VL.2 15 PLIP interactions: 15 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:N.96, A:F.97, A:F.101, A:L.127 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89

1 x 5VL: 2-(2-hydroxyphenyl)phenol(Non-covalent)

5VL.2: 7 residues within 4Å: Chain A: F.21, F.35, Y.38, H.55, T.56, V.59 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.21, A:F.35, A:Y.38, A:H.55, A:V.59, A:V.59 Hydrogen bonds: A:Y.38 pi-Stacking: A:F.21

6 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.4, A:Q.4, A:D.5, A:Q.113, A:S.114 Water bridges: A:D.116 GOL.4: 5 residues within 4Å: Chain A: K.3, I.6, A.7, R.10, D.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.3, A:R.10, A:D.68 GOL.5: 4 residues within 4Å: Chain A: R.10, E.65, D.68, R.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.10, A:R.10, A:E.65, A:R.69 GOL.6: 7 residues within 4Å: Chain A: E.98, F.101, V.102, W.120, D.121, G.124, K.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.98, A:E.98, A:D.121, A:K.125, A:K.125 GOL.7: 5 residues within 4Å: Chain A: R.33, T.93, G.95, N.96, K.99 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.33, A:T.93, A:G.95, A:K.99 Water bridges: A:T.94 GOL.10: 2 residues within 4Å: Chain A: R.14, D.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14, A:D.54

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 5 residues within 4Å: Chain A: D.12, T.15, Y.16, Y.107, Q.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.12

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

PEG.9: 2 residues within 4Å: Chain A: D.68, R.69 No protein-ligand interaction detected (PLIP)

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

SO4.11: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.2, A:K.3 Water bridges: A:G.1, A:Q.4 SO4.12: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yun, D. et al., Oxidation of bisphenol A (BPA) and related compounds by the multifunctional catalytic globin dehaloperoxidase. J.Inorg.Biochem. (2023)

Release Date

2022-11-02

Peptides

Dehaloperoxidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dehaloperoxidase B

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