SMTL ID : 7dlk.3 (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.323, L.326, L.332 Ligands: OXY.2 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:F.185, A:I.225, A:I.225, A:F.244, A:F.244, A:V.274, A:V.274, A:A.277, A:L.306, A:L.306, A:F.308, A:F.319, A:L.323, A:L.326, A:L.332 Hydrogen bonds: A:G.188, A:T.189, A:G.190 Salt bridges: A:K.278, A:R.286 pi-Stacking: A:F.308 pi-Cation interactions: A:R.286 Metal complexes: A:H.273 HEM.10: 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.11 25 PLIP interactions: 25 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.326, 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:R.246, B:K.278 Salt bridges: B:K.278, B:R.286 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, F.308 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.286 OXY.11: 5 residues within 4Å: Chain B: D.187, R.286, L.306 Ligands: HEM.10, VOH.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.187, B:R.286

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 6 residues within 4Å: Chain A: I.231, R.234, S.235, D.239, E.334, Y.335 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:D.239, A:E.334, A:E.334

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: E.354, Q.358, R.359, E.362 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.354 GOL.5: 3 residues within 4Å: Chain A: N.123, L.124, D.125 No protein-ligand interaction detected (PLIP) GOL.6: 3 residues within 4Å: Chain A: P.297, K.298, T.299 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.297 Water bridges: A:T.299, B:E.161 GOL.7: 9 residues within 4Å: Chain A: E.62, Q.63, R.64, N.65, L.68, P.69, P.70, Q.71 Chain B: L.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.64, A:N.65, A:Q.71 Water bridges: A:D.72 GOL.14: 9 residues within 4Å: Chain B: L.53, S.76, L.79, S.80, P.81, L.84, V.144, H.147, A.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.53, B:S.76, B:S.76, B:H.147, B:A.148 GOL.15: 4 residues within 4Å: Chain B: S.235, D.239, E.334, Y.335 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.235, B:Y.335

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

CL.8: 2 residues within 4Å: Chain A: Q.63, R.64 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: P.70 Chain B: D.233 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: P.347, G.348, G.349, I.356, A.357 Ligand excluded by PLIP

1 x VOH: Veratryl alcohol(Non-covalent)

VOH.12: 10 residues within 4Å: Chain B: H.20, L.170, P.179, D.187, G.188, N.191, R.286, R.287, A.288 Ligands: OXY.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.170, B:P.179 Hydrogen bonds: B:D.187, B:N.191, B:A.288 Water bridges: B:H.20 pi-Stacking: B:H.20

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

MPD.13: 6 residues within 4Å: Chain A: L.153, N.154, V.157, V.162 Chain B: Y.301, M.302 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.153, A:V.157, B:Y.301, B:M.302 Water bridges: A:N.154, B:L.229

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
F

B
C

Deferrochelatase/peroxidase

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