SMTL ID : 3fm4.1

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

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

HEM.1: 23 residues within 4Å: Chain A: H.39, E.40, L.42, R.43, T.45, F.46, P.139, E.140, P.141, L.165, L.166, S.168, H.169, I.171, A.172, A.173, A.174, A.175, K.176, V.177, F.186, L.228, S.230 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: 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:L.165, A:L.166, A:L.166, A:A.172, A:A.174, A:V.177, A:F.186, A:F.186 Hydrogen bonds: A:A.173, A:A.175, A:K.176, A:V.177 Salt bridges: A:R.43 pi-Stacking: A:F.46 Metal complexes: A:H.169, H2O.7

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.62, A:S.64, H2O.1, H2O.5 CA.3: 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:D.187, A:D.187, A:T.189, A:V.192, A:D.194

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: D.30, E.36, E.37 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.30, A:D.30, A:E.37, A:E.37, H2O.4 ZN.5: 1 residues within 4Å: Chain A: D.237 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.237, A:D.237, H2O.6 ZN.6: 4 residues within 4Å: Chain A: E.140, D.143 Ligands: CAC.12, CAC.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.140, A:D.143, A:D.143 ZN.8: 1 residues within 4Å: Chain A: H.95 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.95, H2O.6 ZN.9: 4 residues within 4Å: Chain A: H.136, E.140 Ligands: CAC.12, CAC.13 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.136, H2O.5, H2O.10 ZN.10: 3 residues within 4Å: Chain A: E.36, E.40, E.83 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.36, A:E.40, A:E.83, A:E.83, H2O.9

2 x FE: FE (III) ION(Non-covalent)

FE.7: 2 residues within 4Å: Chain A: H.293, D.318 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.293, A:D.318, H2O.12 FE.11: 2 residues within 4Å: Chain A: D.69, K.89 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.69, H2O.1, H2O.4, H2O.10

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.12: 8 residues within 4Å: Chain A: H.136, V.138, E.140, D.143, S.147 Ligands: ZN.6, ZN.9, CAC.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.147 Water bridges: A:H.136 CAC.13: 7 residues within 4Å: Chain A: H.136, E.140, F.142, D.143 Ligands: ZN.6, ZN.9, CAC.12 No protein-ligand interaction detected (PLIP)

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

2009-12-22

Peptides

Versatile peroxidase VPL2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Versatile peroxidase VPL2