SMTL ID : 7pl0.2 (1 other biounit)

Crystal structure of a DyP-type peroxidase 5G5 variant from Bacillus subtilis

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.234, F.238, K.239, D.240, G.241, T.242, G.243, I.278, M.280, F.297, H.326, V.327, V.330, K.331, R.339, L.359, F.361, F.372, M.375, L.376, L.379, L.385, T.389 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:F.238, A:I.278, A:F.297, A:F.297, A:V.327, A:V.330, A:K.331, A:L.359, A:L.359, A:F.361, A:F.361, A:F.372, A:M.375, A:L.376, A:L.379, A:L.385, A:T.389 Hydrogen bonds: A:G.241, A:T.242, A:G.243 Salt bridges: A:K.331, A:R.339 pi-Cation interactions: A:R.339 Metal complexes: A:H.326 HEM.2: 25 residues within 4Å: Chain B: N.234, F.238, K.239, D.240, G.241, T.242, G.243, I.278, M.280, F.297, R.299, H.326, V.327, V.330, K.331, I.337, R.339, L.359, F.361, F.372, M.375, L.376, L.379, L.385, T.389 29 PLIP interactions: 29 interactions with chain B, Hydrophobic interactions: B:F.238, B:I.278, B:I.278, B:F.297, B:F.297, B:V.327, B:V.330, B:I.337, B:L.359, B:F.361, B:F.361, B:F.372, B:M.375, B:L.376, B:L.379, B:L.385, B:T.389 Hydrogen bonds: B:G.241, B:T.242, B:G.243 Water bridges: B:R.299, B:R.299, B:R.299, B:K.331, B:K.331 Salt bridges: B:K.331, B:R.339 pi-Cation interactions: B:R.339 Metal complexes: B:H.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodrigues, C.F. et al., Loops around the Heme Pocket Have a Critical Role in the Function and Stability of Bs DyP from Bacillus subtilis . Int J Mol Sci (2021)

Release Date

2021-10-27

Peptides

Deferrochelatase/peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Deferrochelatase/peroxidase

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