SMTL ID : 7dlk.1 (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: 24 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.326, L.332, T.336 Ligands: OXY.2 24 PLIP interactions: 24 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.308, A:F.319, 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:K.278 Salt bridges: A:K.278, A:R.286 pi-Cation interactions: A:R.286 Metal complexes: A:H.273 HEM.9: 26 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.10, GOL.13 28 PLIP interactions: 28 interactions with chain B, Hydrophobic interactions: B:F.185, B:I.225, B:F.244, B:V.274, B:A.277, B:L.306, B:L.306, B:F.308, B:F.308, B:F.319, B:L.323, B:L.332, B:T.336 Hydrogen bonds: B:G.188, B:T.189, B:G.190 Water bridges: B:R.246, 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.10: 4 residues within 4Å: Chain B: D.187, R.286 Ligands: HEM.9, VOH.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.286

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: L.153, N.154, V.157, V.162 Chain B: Y.301, M.302 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.301, B:M.302, A:L.153, A:V.157, A:V.162 Water bridges: A:A.156

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: L.229, E.230, Y.301, M.302 Chain B: L.153 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.230, A:M.302 Water bridges: A:L.229, B:L.153 GOL.5: 3 residues within 4Å: Chain A: E.3, I.5, P.7 No protein-ligand interaction detected (PLIP) GOL.6: 7 residues within 4Å: Chain A: I.225, L.326, D.330, L.332, N.333, T.336, T.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.327, A:D.330, A:D.330 Water bridges: A:R.223 GOL.12: 3 residues within 4Å: Chain B: N.266, I.268, S.270 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.270 GOL.13: 8 residues within 4Å: Chain B: I.225, L.323, D.330, L.332, N.333, T.336, T.338 Ligands: HEM.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.336, B:T.336, B:T.338 Water bridges: B:R.223, B:R.223, B:T.338

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

CL.7: 3 residues within 4Å: Chain A: P.269, S.270, N.271 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: N.181, L.182, M.227, S.290, G.305, L.306 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 2 residues within 4Å: Chain A: R.44, S.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.44 Salt bridges: A:R.44

1 x VOH: Veratryl alcohol(Non-covalent)

VOH.11: 11 residues within 4Å: Chain B: H.20, L.170, P.179, D.187, G.188, N.191, L.285, R.286, R.287, A.288 Ligands: OXY.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.170, B:P.179 Hydrogen bonds: B:D.187, B:A.288 Water bridges: B:H.20, B:N.191 pi-Stacking: B:H.20

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
A

B
E

Deferrochelatase/peroxidase

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