SMTL ID : 3mm3.1

Dye-decolorizing peroxidase (DyP) D171N in complex with cyanide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: E.165, F.169, L.170, N.171, G.172, I.173, S.174, F.223, Q.225, F.261, R.263, H.308, V.309, T.312, N.313, R.315, R.329, L.354, F.356, E.358, F.367, Q.370, Q.371, I.394, V.420 Ligands: CYN.2 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:E.165, A:F.169, A:F.223, A:F.223, A:Q.225, A:F.261, A:F.261, A:T.312, A:N.313, A:L.354, A:F.356, A:F.367, A:Q.370, A:Q.371, A:I.394, A:V.420 Hydrogen bonds: A:N.171, A:G.172, A:I.173, A:S.174, A:S.174, A:S.174, A:N.313 Water bridges: A:R.263 Salt bridges: A:R.263, A:R.315, A:R.329 pi-Cation interactions: A:R.329 Metal complexes: A:H.308

1 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 4 residues within 4Å: Chain A: N.171, R.329, F.356 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.171, A:R.329, A:S.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshida, T. et al., The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue. Febs J. (2011)

Release Date

2011-04-27

Peptides

DyP: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DyP

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