SMTL ID : 7c73.1

Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in MgCl2 at 2.70 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 24 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, Y.312, T.344, F.347, R.348, G.350, H.351, V.354, L.376, F.380, L.417, L.421, L.433, I.436, R.440 27 PLIP interactions: 26 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:E.258, A:Q.259, A:F.347, A:R.348, A:V.354, A:V.354, A:L.376, A:F.380, A:L.417, A:L.421, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:A.114 Water bridges: A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.348, A:R.440 pi-Stacking: A:H.351 Metal complexes: A:H.351, H2O.2

2 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:D.110, A:T.184, A:F.186, A:S.190 CA.6: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 No protein-ligand interaction detected (PLIP)

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

NAG.3: 6 residues within 4Å: Chain A: N.205, S.208, L.212, A.214, V.215, Q.217 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 NAG.4: 2 residues within 4Å: Chain A: N.332, S.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:S.334 NAG.5: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 angstrom resolution. J.Biol.Inorg.Chem. (2021)

Release Date

2020-06-24

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

Related Entries With Identical Sequence