SMTL ID : 6a6q.1

Crystal structure of a lignin peroxidase isozyme H8 variant that is stable at very acidic pH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

1 x HEB: HEME B/C(Non-covalent)

HEB.1: 24 residues within 4Å: Chain A: H.46, E.47, I.49, R.50, F.53, I.92, P.152, E.153, P.154, L.176, M.179, L.180, A.182, H.183, V.185, A.186, A.187, V.188, N.189, D.190, V.191, F.200, I.242, S.244 27 PLIP interactions: 26 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:R.50, A:F.53, A:F.53, A:F.53, A:F.53, A:F.53, A:P.152, A:P.154, A:L.176, A:M.179, A:A.182, A:A.186, A:V.188, A:F.200, A:I.242 Hydrogen bonds: A:A.187, A:N.189, A:N.189, A:D.190, A:D.190, A:V.191 Water bridges: A:R.50, A:R.50 Salt bridges: A:R.50 pi-Stacking: A:F.200 Metal complexes: A:H.183, H2O.5

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.55, G.73, D.75, S.77 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.55, A:D.75, A:S.77, H2O.1, H2O.4 CA.3: 5 residues within 4Å: Chain A: S.184, D.201, T.203, I.206, D.208 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.201, A:D.201, A:T.203, A:I.206, A:D.208

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: S.20, W.24, V.110, T.111, D.114, T.137 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.111, A:T.111, A:T.137 Water bridges: A:S.20, A:G.138 GOL.5: 7 residues within 4Å: Chain A: C.10, S.11, N.12, C.22, A.23, F.25, D.26 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.11, A:N.12, A:N.12, A:F.25, A:D.26, A:D.26 GOL.6: 4 residues within 4Å: Chain A: E.64, F.69, G.71, G.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pham, L.T.M. et al., In silico-designed lignin peroxidase fromPhanerochaete chrysosporiumshows enhanced acid stability for depolymerization of lignin. Biotechnol Biofuels (2018)

Release Date

2019-01-23

Peptides

Ligninase H8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ligninase H8