SMTL ID : 5twt.1

Characterization of class III peroxidase from switchgrass (Panicum virgatum)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

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

HEM.1: 30 residues within 4Å: Chain A: R.69, A.72, S.73, L.75, R.76, F.79, S.109, R.111, P.175, P.176, P.177, L.184, F.188, L.198, L.201, S.202, A.204, H.205, I.207, G.208, Q.209, A.210, Q.211, N.214, L.248, L.271, S.273, F.301, M.305, M.308 32 PLIP interactions: 31 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:A.72, A:R.76, A:F.79, A:F.79, A:F.79, A:F.79, A:P.175, A:P.177, A:L.184, A:F.188, A:F.188, A:L.198, A:L.201, A:A.204, A:A.210, A:N.214, A:L.248 Hydrogen bonds: A:S.73, A:S.109, A:S.109, A:Q.209, A:Q.209, A:Q.211, A:Q.211, A:N.214 Water bridges: A:R.69, A:R.76 Salt bridges: A:R.69, A:R.76 pi-Cation interactions: A:R.76 Metal complexes: A:H.205, H2O.7

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: T.206, D.249, T.252, T.255, D.257, A.259 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.206, A:T.206, A:D.249, A:T.252, A:T.255 CA.3: 7 residues within 4Å: Chain A: D.81, V.84, Q.85, G.86, D.88, S.90, V.91 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.81, A:V.84, A:G.86, A:D.88, H2O.1

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: M.70, R.111, G.112, F.113, G.114 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.112, A:F.113, A:G.114 Water bridges: A:L.110, A:V.115 SO4.5: 5 residues within 4Å: Chain A: T.251, T.252, P.253, N.254, T.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.253, A:N.254, A:N.254, A:T.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moural, T.W. et al., Characterization of Class III Peroxidases from Switchgrass. Plant Physiol. (2017)

Release Date

2017-01-25

Peptides

Peroxidase Pvi9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peroxidase Pvi9