SMTL ID : 5wv3.1

Crystal structure of bovine lactoperoxidase with a partial Glu258-heme linkage at 2.07 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.110, T.184, F.186, D.188, S.190 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.110, A:T.184, A:T.184, A:F.186, A:S.190

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 22 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, R.255, E.258, Q.259, T.344, F.347, R.348, G.350, H.351, V.354, F.380, L.417, L.433, I.436, R.440 Ligands: BR.19 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Q.105, A:Q.259, A:F.347, A:R.348, A:V.354, A:F.380, A:L.417, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Water bridges: A:R.255, A:R.348, A:R.348, A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.5

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 5 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: OSM.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 NAG.5: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.388, A:K.388 NAG.6: 2 residues within 4Å: Chain A: N.332, V.335 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.335

3 x IOD: IODIDE ION(Non-functional Binders)

IOD.7: 7 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, N.341, V.342, W.452 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain A: N.216, E.218, F.229 Ligands: OSM.21 Ligand excluded by PLIP

10 x OSM: 1-(OXIDOSULFANYL)METHANAMINE(Non-covalent)

OSM.8: 3 residues within 4Å: Chain A: Y.85, L.86, D.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.86, A:D.87 OSM.9: 3 residues within 4Å: Chain A: H.377, T.378, H.429 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.429 OSM.10: 4 residues within 4Å: Chain A: H.565, A.566, F.567, Q.568 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.566, A:F.567 OSM.11: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:R.504, A:R.506, A:R.506 OSM.12: 4 residues within 4Å: Chain A: E.77, N.80, K.81, P.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 OSM.13: 4 residues within 4Å: Chain A: P.461, K.462, T.463, G.466 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.462 OSM.14: 4 residues within 4Å: Chain A: R.76, P.149, K.150, N.419 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.76, A:K.150, A:N.419 OSM.15: 4 residues within 4Å: Chain A: E.50, F.59, R.67, N.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.68, A:N.68 OSM.16: 7 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, I.559, T.560, K.561 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.397, A:T.560, A:T.560, A:K.561 OSM.21: 8 residues within 4Å: Chain A: V.215, N.216, Q.217, E.218, P.228, F.229, N.231 Ligands: IOD.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.217, A:E.218, A:F.229, A:F.229

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 4 residues within 4Å: Chain A: T.23, I.24, T.25, P.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.24, A:T.25, A:T.25 GOL.22: 3 residues within 4Å: Chain A: S.198, L.199, R.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.202

1 x BR: BROMIDE ION(Non-covalent)

BR.19: 4 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Structural basis of activation of mammalian heme peroxidases. Prog. Biophys. Mol. Biol. (2018)

Release Date

2017-02-15

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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