SMTL ID : 7mnh.1

V59W mutant of Dehaloperoxidase A from Amphitrite ornata treated with Fluoride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: F.25, E.32, Y.35, F.36, H.56, K.59, W.60, L.63, M.64, L.84, M.87, Q.89, H.90, L.93, N.97, F.98, L.101, L.128 19 PLIP interactions: 18 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.25, A:F.36, A:W.60, A:W.60, A:L.63, A:M.64, A:L.84, A:Q.89, A:L.93, A:L.93, A:N.97, A:F.98, A:L.101, A:L.128 Salt bridges: A:H.56, A:H.56, A:K.59 Metal complexes: A:H.90, H2O.1 HEM.3: 17 residues within 4Å: Chain B: F.25, E.32, Y.35, F.36, H.56, K.59, W.60, L.63, M.64, L.84, M.87, Q.89, H.90, L.93, N.97, F.98, L.128 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.25, B:F.36, B:W.60, B:W.60, B:L.63, B:M.64, B:L.84, B:Q.89, B:L.93, B:L.93, B:N.97, B:F.98, B:L.128 Hydrogen bonds: B:Q.89 Water bridges: B:K.37, B:K.59 Salt bridges: B:H.56, B:H.56, B:K.59 pi-Stacking: B:W.60 Metal complexes: B:H.90, H2O.7

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

SO4.2: 4 residues within 4Å: Chain A: G.2, F.3, K.4, D.117 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.3, A:K.4, A:D.117 Water bridges: A:Q.5, A:S.120 SO4.4: 7 residues within 4Å: Chain A: R.33, V.40, G.41 Chain B: G.2, F.3, K.4, D.117 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:G.41, B:F.3, B:K.4, B:D.117 Salt bridges: A:R.33 Water bridges: B:G.2, B:Q.5, B:S.120, B:S.120, B:S.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, M.K. et al., A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study. J Porphyr Phthalocyanines (2021)

Release Date

2021-11-24

Peptides

Dehaloperoxidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase A