SMTL ID : 3q3u.1

Trametes cervina lignin peroxidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: E.37, H.40, E.41, V.43, R.44, F.47, P.146, D.147, P.148, I.155, L.172, L.173, S.175, H.176, I.178, A.179, A.180, Q.181, Y.182, E.183, V.184, F.193, L.234, S.236, F.264, M.268 33 PLIP interactions: 32 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:H.40, A:V.43, A:R.44, A:F.47, A:F.47, A:F.47, A:F.47, A:P.146, A:P.148, A:I.155, A:L.172, A:L.172, A:L.173, A:A.179, A:Q.181, A:V.184, A:F.193, A:F.193, A:L.234, A:F.264 Hydrogen bonds: A:E.41, A:A.180, A:Y.182, A:E.183, A:V.184 Water bridges: A:H.40, A:H.40, A:R.44 Salt bridges: A:H.40, A:R.44 pi-Stacking: A:F.193 Metal complexes: A:H.176, H2O.3

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 3 residues within 4Å: Chain A: F.63, Q.138, P.139 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.138 Hydrogen bonds: A:Q.138 Water bridges: A:F.63

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.49, G.67, D.69, S.71 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.49, A:D.69, A:S.71, H2O.2, H2O.3 CA.4: 5 residues within 4Å: Chain A: S.177, D.194, T.196, V.199, D.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.194, A:D.194, A:T.196, A:V.199, A:D.201

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: W.18, A.131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miki, Y. et al., Crystallographic, kinetic, and spectroscopic study of the first ligninolytic peroxidase presenting a catalytic tyrosine. J.Biol.Chem. (2011)

Release Date

2011-03-02

Peptides

Lignin peroxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lignin peroxidase