SMTL ID : 3fmu.1

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

monomer

Ligands

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

HEM.1: 31 residues within 4Å: Chain A: H.39, E.40, L.42, R.43, T.45, F.46, P.139, E.140, P.141, I.148, M.152, V.162, L.165, L.166, S.168, H.169, I.171, A.172, A.173, A.174, D.175, K.176, V.177, F.186, L.228, S.230, L.234, F.258, M.262, M.265 Ligands: ZN.9 27 PLIP interactions: 26 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:F.46, A:P.139, A:P.141, A:I.148, A:L.165, A:L.166, A:A.172, A:A.174, A:V.177, A:F.186, A:F.186, A:L.228 Hydrogen bonds: A:H.39, A:A.173, A:D.175, A:K.176, A:V.177 Water bridges: A:R.43 Salt bridges: A:R.43 Metal complexes: A:H.169, H2O.13

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.48, G.60, D.62, S.64, I.65 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.48, A:D.62, A:S.64, H2O.2, H2O.5 CA.3: 7 residues within 4Å: Chain A: S.170, D.187, T.189, P.190, V.192, D.194, Q.196 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

8 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: D.30, 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.3 ZN.5: 5 residues within 4Å: Chain A: V.145, D.146, D.237, P.238, Q.239 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.237, A:D.237, H2O.3, H2O.11, H2O.13 ZN.6: 4 residues within 4Å: Chain A: E.140, F.142, D.143 Ligands: CAC.17 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.143, A:D.143, H2O.12 ZN.8: 3 residues within 4Å: Chain A: I.20, H.95, N.96 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.95, H2O.5, H2O.20 ZN.9: 4 residues within 4Å: Chain A: E.36, E.40, D.175 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) ZN.10: 2 residues within 4Å: Chain A: H.136 Ligands: CAC.17 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.136, H2O.11 ZN.11: 5 residues within 4Å: Chain A: E.36, E.40, E.83 Ligands: ZN.12, FE.13 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.36, A:E.40, H2O.10 ZN.12: 5 residues within 4Å: Chain A: E.36, E.37, E.40, E.83 Ligands: ZN.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.36, A:E.40, A:E.40, H2O.13

5 x FE: FE (III) ION(Non-covalent)(Non-functional Binders)

FE.7: 3 residues within 4Å: Chain A: H.293, P.295, D.318 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.293, A:D.318, H2O.6, H2O.6, H2O.6, H2O.15 FE.13: 3 residues within 4Å: Chain A: E.83, D.175 Ligands: ZN.11 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.83, A:D.175, H2O.5, H2O.10, H2O.10, H2O.11 FE.14: 3 residues within 4Å: Chain A: D.69, T.70, K.89 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.69, H2O.11, H2O.11, H2O.16 FE.15: 1 residues within 4Å: Ligands: FE.16 No protein-ligand interaction detected (PLIP) FE.16: 2 residues within 4Å: Chain A: D.128 Ligands: FE.15 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.128, H2O.20

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.17: 8 residues within 4Å: Chain A: H.136, V.138, P.139, D.143, S.147, R.151 Ligands: ZN.6, ZN.10 6 PLIP interactions: 6 interactions with chain A Water bridges: A:H.136, A:H.136, A:V.138, A:E.140, A:S.147, A:S.147

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