SMTL ID : 3fjw.1 (1 other biounit)

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x BMA- MAN: alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose(Post Translational Modification)

BMA-MAN.1: 9 residues within 4Å: Chain A: S.188, T.189, H.293, P.295, A.296, D.318, T.323, S.324, P.326 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.188, A:S.188, A:H.293, A:A.296, A:D.318, A:S.188

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

HEM.2: 25 residues within 4Å: Chain A: E.36, H.39, E.40, L.42, R.43, T.45, F.46, P.139, E.140, P.141, I.148, L.165, L.166, S.168, H.169, A.172, A.173, A.174, D.175, K.176, V.177, F.186, L.228, S.230 Ligands: MN.5 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:H.39, A:L.42, A:L.42, A:R.43, A:F.46, A:F.46, A:F.46, A:P.139, A:P.141, A:I.148, A:L.165, A:L.166, A:L.166, A:A.172, A:A.174, A:F.186, A:F.186, A:L.228 Hydrogen bonds: A:A.173, A:A.173, A:D.175, A:K.176, A:V.177 Salt bridges: A:H.39, A:R.43 pi-Stacking: A:F.46 Metal complexes: A:H.169

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.48, G.60, D.62, S.64 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.48, A:D.48, A:D.62, H2O.3, H2O.7 CA.4: 5 residues within 4Å: Chain A: S.170, D.187, T.189, V.192, D.194 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.170, A:D.187, A:T.189, A:V.192, A:D.194

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 4 residues within 4Å: Chain A: E.36, E.40, D.175 Ligands: HEM.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.36, A:E.40, A:D.175, H2O.5, H2O.6

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

NAG.6: 1 residues within 4Å: Chain A: N.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.96

3 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.7: 5 residues within 4Å: Chain A: C.242, Q.245, S.246, A.309, T.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.242, A:Q.245 MAN.8: 5 residues within 4Å: Chain A: Q.223, G.224, S.324, V.325, P.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.223, A:V.325 MAN.9: 3 residues within 4Å: Chain A: R.119, P.283, T.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.119, A:T.284 Water bridges: A:D.280, A:I.282, A:T.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piontek, K. et al., Structural and Site-directed Mutagenesis Study of Versatile Peroxidase Oxidizing both Mn(II) and Aromatic Substrates. To be Published

Release Date

2009-12-15

Peptides

Versatile peroxidase VPL2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Versatile peroxidase VPL2

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