SMTL ID : 7kfm.1

Room temperature oxyferrous Dehaloperoxidase B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 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, 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: OXY.3, PG0.4 15 PLIP interactions: 15 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:L.100, A:L.127 Salt bridges: A:H.55, A:H.55 Metal complexes: A:H.89 HEM.5: 14 residues within 4Å: Chain B: N.34, F.35, K.36, H.55, K.58, V.59, L.62, M.63, M.86, Q.88, H.89, L.92, F.97, L.100 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:N.34, B:F.35, B:F.35, B:K.58, B:V.59, B:V.59, B:L.62, B:L.92, B:L.92, B:F.97, B:L.100 Hydrogen bonds: B:K.36 pi-Stacking: B:H.55, B:H.89 pi-Cation interactions: B:H.89 Metal complexes: B:H.55

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

SO4.2: 3 residues within 4Å: Chain A: K.32, V.39, G.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.40 Salt bridges: A:K.32 SO4.6: 3 residues within 4Å: Chain B: K.32, V.39, G.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.40 Salt bridges: B:K.32

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 4 residues within 4Å: Chain A: H.55, V.59 Ligands: HEM.1, PG0.4 No protein-ligand interaction detected (PLIP)

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.4: 7 residues within 4Å: Chain A: F.21, F.35, H.55, V.59, M.63 Ligands: HEM.1, OXY.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moreno-Chicano, T. et al., Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature. Iucrj (2022)

Release Date

2021-10-20

Peptides

Dehaloperoxidase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase B

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