SMTL ID : 6kmm.2 (2 other biounits)

Crystal Structure of HEPES bound Dye Decolorizing peroxidase from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 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 25 PLIP interactions: 25 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.319, A:M.322, 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 Salt bridges: A:R.246, A:K.278, A:R.286 pi-Stacking: A:F.308 pi-Cation interactions: A:R.286 Metal complexes: A:H.273 HEM.5: 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.6 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.308, B:F.319, B:M.322, 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:K.278, B:K.278, 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, L.306 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.187, A:R.286 OXY.6: 4 residues within 4Å: Chain B: D.187, R.286, L.306 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.286

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: T.292, E.293, G.294, M.302 Chain B: Y.25, K.167 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.292, A:G.294 Water bridges: B:K.167

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

MPD.4: 7 residues within 4Å: Chain A: E.230, Y.301, M.302 Chain B: L.153, N.154, V.157, V.162 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.301, A:M.302, B:L.153, B:V.162 Water bridges: A:L.229, B:N.154 MPD.10: 7 residues within 4Å: Chain A: L.153, N.154, V.157, V.162 Chain B: L.229, Y.301, M.302 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.229, B:Y.301, B:M.302, A:V.157 Hydrogen bonds: B:M.302

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

EPE.7: 6 residues within 4Å: Chain B: I.231, R.234, S.235, D.239, E.334, Y.335 5 PLIP interactions: 5 interactions with chain B Water bridges: B:E.334 Salt bridges: B:R.234, B:D.239, B:E.334, B:E.334

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain B: R.44, S.48 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.44, B:S.48 Water bridges: B:S.48, B:G.353

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

PO4.9: 3 residues within 4Å: Chain B: D.38, G.158, T.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.159, B:T.159

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

CL.11: 1 residues within 4Å: Chain B: S.198 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dhankhar, P. et al., Characterization of dye-decolorizing peroxidase from Bacillus subtilis. Arch.Biochem.Biophys. (2020)

Release Date

2020-10-21

Peptides

Deferrochelatase/peroxidase EfeB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Deferrochelatase/peroxidase EfeB

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