SMTL ID : 5ag1.1 (1 other biounit)

DyP-type peroxidase of Auricularia auricula-judae (AauDyPI) with meso- nitrated heme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: Q.276, R.277, N.280, T.317, P.318 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.317

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.2: 3 residues within 4Å: Chain A: S.284, H.285, A.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.286

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: D.124, D.127, Q.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.124 Water bridges: A:D.124 GOL.4: 8 residues within 4Å: Chain A: R.152, E.156, M.161, F.162, G.163, V.221, N.225, K.255 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.152, A:R.152, A:N.225, A:K.255 Water bridges: A:G.163, A:N.225, A:K.255 GOL.5: 3 residues within 4Å: Chain A: A.270, D.274, R.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.277, A:R.277 GOL.6: 5 residues within 4Å: Chain A: G.194, A.195, T.196, N.197, D.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.194, A:N.197, A:N.197

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

NAG.7: 5 residues within 4Å: Chain A: K.226, D.230, A.345, S.346, N.347 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.226, A:D.230, A:A.345, A:N.347 NAG.8: 3 residues within 4Å: Chain A: N.413, S.415, A.416 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.413 Water bridges: A:S.415

1 x N7H: DELTA-MESO NITROHEME(Covalent)

N7H.9: 26 residues within 4Å: Chain A: E.160, F.162, F.164, L.165, D.166, G.167, I.168, A.169, L.217, Q.219, V.251, R.253, H.302, I.303, T.306, R.307, R.309, R.330, L.355, F.357, F.368, L.371, Q.372, I.395, I.396 Ligands: NO2.11 36 PLIP interactions: 36 interactions with chain A, Hydrophobic interactions: A:F.162, A:F.164, A:A.169, A:L.217, A:L.217, A:Q.219, A:V.251, A:I.303, A:T.306, A:R.307, A:L.355, A:L.355, A:F.357, A:F.357, A:F.357, A:F.368, A:L.371, A:L.371, A:I.395, A:I.396, A:I.396 Hydrogen bonds: A:D.166, A:G.167, A:I.168, A:A.169 Water bridges: A:A.169, A:R.253, A:R.307, A:R.307, A:R.309 Salt bridges: A:R.253, A:R.307, A:R.309, A:R.330 pi-Cation interactions: A:R.330 Metal complexes: A:H.302

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.10: 3 residues within 4Å: Chain A: N.28, D.29, S.139 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.29, A:D.29

1 x NO2: NITRITE ION(Non-covalent)

NO2.11: 5 residues within 4Å: Chain A: D.166, R.330, L.355, F.357 Ligands: N7H.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.330 Water bridges: A:G.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strittmatter, E. et al., Crystallographic Trapping of a Covalently Modified Heme in a Dye-Decolorizing Peroxidase. To be Published

Release Date

2016-03-02

Peptides

DYE-DECOLORIZING PEROXIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DYE-DECOLORIZING PEROXIDASE

Related Entries With Identical Sequence