SMTL ID : 6i7f.1

Dehaloperoxidase B from Amphitrite ornata - complex with 2,4-dichlorophenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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, N.34, F.35, D.54, 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: 5JC.2 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:K.58, A:V.59, 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:F.97, A:L.100, A:L.127 Hydrogen bonds: A:H.55 Salt bridges: A:K.58 pi-Stacking: A:H.55 Metal complexes: A:H.89 HEM.5: 18 residues within 4Å: Chain B: 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, L.127 Ligands: 5JC.6 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:F.24, B:F.35, B:F.35, B:V.59, B:L.62, B:L.62, B:L.83, B:Q.88, B:L.92, B:N.96, B:L.127 Salt bridges: B:H.55, B:H.55 Metal complexes: B:H.89

2 x 5JC: 2,4-dichlorophenol(Non-covalent)

5JC.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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.21, A:T.56, A:V.59, A:L.100 pi-Stacking: A:F.21 5JC.6: 9 residues within 4Å: Chain B: A.17, F.21, F.35, H.55, T.56, V.59, F.60, L.100 Ligands: HEM.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.21, B:V.59, B:L.100 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 6 PLIP interactions: 6 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 SO4.4: 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

Moreno-Chicano, T. et al., High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography. Iucrj (2019)

Release Date

2019-11-20

Peptides

Dehaloperoxidase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase B

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