SMTL ID : 7e5q.1

Crystal Structure of Dye Decolorizing peroxidase from Bacillus subtilis at acidic pH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 26 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, EDO.3 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:F.185, A:I.225, 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:M.322, A:L.323, A:L.326, A:L.332, A:T.336 Hydrogen bonds: A:D.187, A:G.188, A:T.189, A:G.190 Water bridges: A:R.246, A:R.246, A:R.246, A:Q.283 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.24: 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.25, GOL.35 27 PLIP interactions: 27 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:L.323, B:L.326, B:L.332, B:T.336 Hydrogen bonds: B:D.187, B:G.188, B:T.189, B:G.190 Water bridges: B:R.246, B:R.246, B:R.246 Salt bridges: 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: 7 residues within 4Å: Chain A: D.187, R.286, A.288, L.306, F.308 Ligands: HEM.1, EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.286 OXY.25: 6 residues within 4Å: Chain B: D.187, R.286, A.288, F.308 Ligands: HEM.24, EDO.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.286

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: I.225, L.326, D.330, N.333, T.336 Ligands: HEM.1 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: A.19, H.20 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: Q.192 Ligands: PEG.13 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: K.11, H.12, D.197, N.201, W.205 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: V.6, P.7, Y.9, G.10, H.12, A.14 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: Y.9, G.10, K.11, C.350, K.351, K.352 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: T.32, A.33, K.34, D.38 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: A.118, D.122, L.124 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: H.20, L.170, D.187, G.188, R.286, R.287, A.288 Ligands: OXY.2 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: L.153, N.154, V.157, V.162 Chain B: E.230, Y.301, M.302 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain B: H.20, L.170, P.179, D.187, G.188, R.286, R.287, A.288 Ligands: OXY.25 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: V.6, P.7, Y.9, G.10, H.12, A.14 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: A.19, H.20, T.194 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: T.17, T.18, T.194 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: T.32, V.157, G.158, C.160, E.161 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: P.321, K.324, A.325 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain B: L.265, N.266, I.268 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: K.278, G.281, K.282, Q.283 Ligand excluded by PLIP

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.12: 6 residues within 4Å: Chain A: L.237, E.241, R.247, K.248, S.249, S.250 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.248, A:S.249, A:S.249, A:S.249, A:S.249, A:S.250 Salt bridges: A:R.247 CIT.34: 6 residues within 4Å: Chain B: L.237, E.241, R.247, K.248, S.249, S.250 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.248, B:S.249, B:S.249, B:S.250 Salt bridges: B:R.247

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 5 residues within 4Å: Chain A: T.260, P.262, K.278 Ligands: EDO.5, NA.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.260 PEG.14: 4 residues within 4Å: Chain A: K.111, S.208, G.209 Ligands: CL.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.111, A:S.208 PEG.15: 4 residues within 4Å: Chain A: E.293, L.295, P.297 Ligands: NA.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.293, A:L.295

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

NA.16: 4 residues within 4Å: Chain A: P.262, V.263, K.278 Ligands: PEG.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.263, A:K.278 NA.36: 4 residues within 4Å: Chain A: L.295 Chain B: F.164, V.165 Ligands: PEG.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.165, B:V.165, A:L.295 NA.37: 6 residues within 4Å: Chain A: Y.25, K.167 Chain B: T.292, E.293, G.294, M.302 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.167, B:G.294 NA.38: 3 residues within 4Å: Chain B: Y.9, K.351, K.352 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.352 NA.39: 3 residues within 4Å: Chain B: T.215, G.348, G.349 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.215 Water bridges: B:G.349 NA.40: 3 residues within 4Å: Chain B: K.97, D.98, G.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.96, B:G.99 NA.41: 1 residues within 4Å: Chain B: R.180 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.78, B:R.180 NA.42: 5 residues within 4Å: Chain B: I.225, N.333, T.336, T.338 Ligands: GOL.35 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.336, B:T.338, B:T.338 Water bridges: B:T.338

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

CL.17: 4 residues within 4Å: Chain A: F.164, V.165 Chain B: G.294, L.295 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: P.7, F.8, Y.9 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: Q.207, S.208, K.313 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: K.111, H.112, N.314 Ligands: PEG.14 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain A: T.292, E.293, G.294 Chain B: Y.25, K.167 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain A: T.17, T.194 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain A: E.293 Chain B: E.293 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain B: D.296, T.299 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain B: P.262, V.263, K.278 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.35: 9 residues within 4Å: Chain B: R.223, H.273, L.323, L.326, S.327, D.330, N.333 Ligands: HEM.24, NA.42 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.223, B:H.273, B:D.330, B:N.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dhankhar, P. et al., Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis. Proteins (2022)

Release Date

2022-08-24

Peptides

Deferrochelatase/peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deferrochelatase/peroxidase

Related Entries With Identical Sequence