SMTL ID : 7rmu.1

Structure of Thermomonospora curvata heme-containing DyP-type peroxidase with a modified axial ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 23 residues within 4Å: Chain A: N.208, Q.212, L.213, D.214, G.215, T.216, V.217, I.250, M.252, R.271, H.306, I.307, A.310, H.311, M.319, R.321, L.340, F.342, V.356, Q.357, L.360, L.367, T.371 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:Q.212, A:V.217, A:I.250, A:I.250, A:I.307, A:A.310, A:L.340, A:F.342, A:F.342, A:V.356, A:L.360, A:L.367, A:T.371 Hydrogen bonds: A:D.214, A:G.215, A:T.216, A:V.217 Water bridges: A:R.271, A:R.271, A:V.312 Salt bridges: A:R.271, A:H.311, A:R.321 pi-Stacking: A:F.342 pi-Cation interactions: A:R.321 HEM.9: 23 residues within 4Å: Chain B: N.208, Q.212, L.213, D.214, G.215, T.216, V.217, I.250, M.252, R.271, H.306, I.307, A.310, H.311, M.319, R.321, L.340, F.342, V.356, Q.357, L.360, L.367, T.371 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:Q.212, B:V.217, B:I.250, B:I.250, B:I.307, B:A.310, B:L.340, B:F.342, B:F.342, B:V.356, B:L.360, B:L.367, B:T.371 Hydrogen bonds: B:G.215, B:T.216, B:V.217 Water bridges: B:R.271, B:R.271, B:V.312 Salt bridges: B:R.271, B:H.311, B:R.321 pi-Stacking: B:F.342 pi-Cation interactions: B:R.321

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.70, K.71, R.185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.71, A:G.72 Salt bridges: A:R.70, A:R.185 SO4.3: 4 residues within 4Å: Chain A: P.45, F.46, H.47, Q.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.46, A:H.47, A:H.47 Salt bridges: A:H.47 SO4.4: 2 residues within 4Å: Chain A: R.80, R.83 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.83 SO4.5: 2 residues within 4Å: Chain A: R.91, R.96 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.96 Salt bridges: A:R.91, A:R.96 SO4.6: 1 residues within 4Å: Chain A: R.187 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.187 SO4.7: 3 residues within 4Å: Chain A: R.272, T.274, S.275 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.274, A:T.274, A:S.275, A:S.275 Water bridges: A:L.273 SO4.8: 3 residues within 4Å: Chain A: H.283, E.284, H.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.284, A:E.284, A:H.285 Salt bridges: A:H.285 SO4.10: 3 residues within 4Å: Chain B: R.70, K.71, R.185 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.71, B:G.72 Salt bridges: B:R.70, B:R.185 SO4.11: 4 residues within 4Å: Chain B: P.45, F.46, H.47, Q.94 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.46, B:H.47, B:H.47 Salt bridges: B:H.47 SO4.12: 2 residues within 4Å: Chain B: R.80, R.83 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.83 SO4.13: 2 residues within 4Å: Chain B: R.91, R.96 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.96 Salt bridges: B:R.91, B:R.96 SO4.14: 1 residues within 4Å: Chain B: R.187 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.187 SO4.15: 3 residues within 4Å: Chain B: R.272, T.274, S.275 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.274, B:T.274, B:S.275, B:S.275 Water bridges: B:L.273, B:T.274 SO4.16: 3 residues within 4Å: Chain B: H.283, E.284, H.285 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.284, B:E.284, B:E.284, B:H.285 Salt bridges: B:H.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khadka, S. et al., Structure of Thermomonospora curvata heme-containing DyP-type peroxidase with a modified axial ligand. To Be Published

Release Date

2022-08-31

Peptides

DyP-type Peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DyP-type Peroxidase

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