SMTL ID : 5ag0.1 (1 other biounit)

DyP-type peroxidase of Auricularia auricula-judae (AauDyPI) crystallized at pH 6.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: P.181, 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 HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.2: 27 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, V.424 Ligands: FMT.6 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:T.306, A:R.307, A:L.355, A:L.355, A:F.357, A:F.357, A:F.368, A:L.371, A:I.395, A:I.396, A:I.396, A:V.424 Hydrogen bonds: A:D.166, A:G.167, A:I.168, A:A.169, A:I.303 Water bridges: A:R.253, A:R.307, A:R.307, A:R.309, A:R.309 Salt bridges: A:R.253, A:R.307, A:R.309, A:R.330 pi-Cation interactions: A:H.302, A:R.330 Metal complexes: A:H.302

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

NAG.3: 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.4: 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 CAC: CACODYLATE ION(Non-covalent)

CAC.5: 3 residues within 4Å: Chain A: S.284, H.285, A.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.286 Water bridges: A:H.296

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

FMT.6: 6 residues within 4Å: Chain A: D.166, R.330, L.355, F.357 Ligands: HEM.2, GOA.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.330 Water bridges: A:G.332 FMT.7: 3 residues within 4Å: Chain A: K.97, A.379, L.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.97

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: S.1, L.2, N.3, I.7, A.195, V.207, G.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.3 GOL.10: 3 residues within 4Å: Chain A: D.124, D.127, Q.128 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.127 GOL.11: 6 residues within 4Å: Chain A: D.40, V.44, Q.129, S.132, I.133, T.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.132, A:S.132, A:T.136, A:T.136 GOL.12: 6 residues within 4Å: Chain A: G.167, I.168, G.272, A.273, A.275, N.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.273, A:N.278 Water bridges: A:I.168 GOL.13: 7 residues within 4Å: Chain A: G.194, A.195, T.196, N.197, D.198 Ligands: GOL.14, GOL.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.194, A:N.197, A:D.198 Water bridges: A:G.194 GOL.14: 2 residues within 4Å: Chain A: P.199 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.199, A:T.201 GOL.15: 3 residues within 4Å: Chain A: G.194, V.207 Ligands: GOL.13 No protein-ligand interaction detected (PLIP) GOL.16: 5 residues within 4Å: Chain A: S.204, W.205, V.207, P.436, S.438 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.207, A:S.438 GOL.17: 7 residues within 4Å: Chain A: N.225, L.228, L.229, Q.240, A.243, D.244, K.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.240, A:A.243, A:D.244, A:K.255 Water bridges: A:N.225

1 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.9: 7 residues within 4Å: Chain A: D.166, G.167, Q.170, R.330, S.331, G.332 Ligands: FMT.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.166, A:Q.170, A:R.330, A:G.332, A:G.332 Water bridges: A:S.331 Salt bridges: A:R.330

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

2016-03-09

Peptides

DYE-DECOLORIZING PEROXIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DYE-DECOLORIZING PEROXIDASE

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