SMTL ID : 3vxj.1

Dye-decolorizing peroxidase (DyP) complex with 2,6-dimethoxyphenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: E.165, F.169, L.170, D.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 30 PLIP interactions: 29 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:E.165, A:F.169, A:F.223, A:F.223, A:Q.225, A:T.312, A:N.313, A:L.354, A:F.356, A:F.367, A:Q.370, A:I.394, A:V.420 Hydrogen bonds: A:D.171, A:D.171, A:G.172, A:I.173, A:S.174, A:S.174, A:N.313 Water bridges: A:S.174, A:S.174, A:R.263, 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, H2O.7

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain A: N.246 No protein-ligand interaction detected (PLIP)

2 x 3DM: 2,6-dimethoxyphenol(Non-covalent)

3DM.3: 11 residues within 4Å: Chain A: G.188, A.190, F.291, D.292, N.313, R.315, L.318, G.320, P.321, V.322, H.326 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.315 Hydrogen bonds: A:N.313, A:R.315, A:H.326 Water bridges: A:V.322 3DM.4: 4 residues within 4Å: Chain A: T.298, S.383, K.384, P.385 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.385

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 8 residues within 4Å: Chain A: F.167, F.230, N.231, T.234, A.253, E.254, G.257, K.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.265 Salt bridges: A:E.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugano, Y. et al., Dye-decolorizing peroxidase (DyP) complex with 2,6-dimethoxyphenol. to be published

Release Date

2012-11-07

Peptides

DyP: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DyP

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