SMTL ID : 7dlk.2 (2 other biounits)

Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: N.181, F.185, K.186, D.187, G.188, T.189, G.190, I.225, M.227, F.244, R.246, H.273, V.274, A.277, K.278, R.286, L.306, F.308, F.319, M.322, L.323, L.326, L.332, T.336 Ligands: OXY.2 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:F.185, A:I.225, A:F.244, A:V.274, A:A.277, A:L.306, A:L.306, A:F.308, A:F.308, A:F.319, A:M.322, A:L.323, A:L.326, A:L.332, A:T.336 Hydrogen bonds: A:G.188, A:T.189, A:G.190 Water bridges: A:R.246, A:R.246, A:R.246, A:K.278, A:K.278, A:K.278 Salt bridges: A:K.278, A:R.286 Metal complexes: A:H.273 HEM.6: 25 residues within 4Å: Chain B: N.181, F.185, K.186, D.187, G.188, T.189, G.190, I.225, M.227, F.244, R.246, H.273, V.274, A.277, K.278, R.286, L.306, F.308, F.319, M.322, L.323, L.326, L.332, T.336 Ligands: OXY.7 29 PLIP interactions: 29 interactions with chain B, Hydrophobic interactions: B:F.185, B:I.225, B:F.244, B:V.274, B:A.277, B:K.278, B:L.306, B:L.306, B:F.308, B:F.308, B:F.319, B:L.323, B:L.326, B:L.332, B:T.336 Hydrogen bonds: B:G.188, B:T.189, B:G.190 Water bridges: B:R.246, B:K.278, B:K.278, B:K.278, B:K.278 Salt bridges: B:R.246, B:K.278, B:R.286 pi-Stacking: B:F.308 pi-Cation interactions: B:R.286 Metal complexes: B:H.273

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 4 residues within 4Å: Chain A: D.187, R.286, L.306 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.286 OXY.7: 5 residues within 4Å: Chain B: D.187, R.286, L.306, F.308 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.286

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: N.121, D.122, I.225, N.333, T.336, Q.337, T.338 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.122, A:T.336, A:T.336, A:T.338 Water bridges: A:N.333 GOL.8: 6 residues within 4Å: Chain A: L.229, E.230, Y.301, M.302 Chain B: L.153, N.154 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.150, B:L.153 Water bridges: B:N.154, A:E.230, A:M.302

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: L.116, S.341, A.342 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: S.198 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: D.330, N.333 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dhankhar, P. et al., Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol. Int.J.Biol.Macromol. (2021)

Release Date

2021-11-03

Peptides

Deferrochelatase/peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
B

Deferrochelatase/peroxidase

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