SMTL ID : 3lb2.1 (1 other biounit)

Two-site competitive inhibition in dehaloperoxidase-hemoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 20 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, M.86, Q.88, H.89, L.92, N.96, F.97, L.100, L.127 Ligands: BML.2 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:V.59, A:L.62, A:L.62, A:L.83, A:Q.88, A:L.92, A:N.96, A:F.97, A:L.127 Water bridges: A:N.37, A:Y.38, A:Y.38, A:K.58, A:Q.88 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89 HEM.5: 19 residues within 4Å: Chain B: 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: BML.6 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.24, B:F.35, B:F.35, B:K.58, B:V.59, B:V.59, B:L.62, B:M.63, B:L.83, B:Q.88, B:L.92, B:L.92, B:N.96, B:F.97, B:L.100, B:L.127 Salt bridges: B:K.51, B:H.55, B:H.55, B:K.58 Metal complexes: B:H.89

2 x BML: 4-BROMOPHENOL(Non-covalent)

BML.2: 7 residues within 4Å: Chain A: F.21, F.35, Y.38, H.55, T.56, V.59 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:V.59, A:V.59 pi-Stacking: A:F.35 BML.6: 7 residues within 4Å: Chain B: F.21, F.35, H.55, T.56, V.59, L.100 Ligands: HEM.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.35, B:T.56, B:V.59, B:V.59 Hydrogen bonds: B:H.55 Water bridges: B:T.56 pi-Stacking: B:F.21

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

SO4.3: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.2, A:K.3, A:D.116 SO4.4: 7 residues within 4Å: Chain A: R.32, V.39, G.40 Chain B: G.1, F.2, K.3, D.116 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.2, B:K.3, B:D.116, A:G.40 Water bridges: B:G.1, B:Q.4, B:S.119, B:S.119, B:S.119 Salt bridges: A:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, M.K. et al., Internal binding of halogenated phenols in dehaloperoxidase-hemoglobin inhibits peroxidase function. Biophys.J. (2010)

Release Date

2010-11-24

Peptides

DEHALOPEROXIDASE A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DEHALOPEROXIDASE A

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