SMTL ID : 6l5g.1

Crystal structure of yak lactoperoxidase with disordered heme moiety at 2.50 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: 8 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217, W.220 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: N.95, R.96, I.315 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.95 Hydrogen bonds: A:R.96 Water bridges: A:R.96 NAG.3: 3 residues within 4Å: Chain A: N.241, A.244, W.384 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.241 NAG.4: 2 residues within 4Å: Chain A: N.332, V.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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

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

HEM.6: 23 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, H.109, D.112, R.255, E.258, Q.259, T.344, F.347, R.348, G.350, H.351, V.354, L.376, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: K.7 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:Q.259, A:F.347, A:F.347, A:F.347, A:R.348, A:V.354, A:V.354, A:L.376, A:F.380, A:L.417, A:L.433, A:L.433, A:I.436 Water bridges: A:R.255 Salt bridges: A:H.109, A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.3

2 x K: POTASSIUM ION(Non-covalent)

K.7: 3 residues within 4Å: Chain A: H.109, R.255 Ligands: HEM.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.109, H2O.3, H2O.12 K.8: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 2 residues within 4Å: Chain A: H.222, H.558 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.222, A:H.558

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: N.230, P.236, C.248, F.249, F.254, F.381, P.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.230 Water bridges: A:F.249 GOL.11: 8 residues within 4Å: Chain A: E.116, P.159, F.160, F.161, Q.423, H.426, F.431, I.436 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.116, A:F.161, A:R.440 Water bridges: A:T.425, A:T.425, A:T.425 GOL.12: 4 residues within 4Å: Chain A: P.375, H.377, E.416, K.420 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.416 GOL.13: 6 residues within 4Å: Chain A: L.92, D.93, Q.94, N.95, L.406, R.506 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.92, A:Q.94, A:R.506 GOL.14: 2 residues within 4Å: Chain A: E.50, S.451 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.50 Water bridges: A:S.451

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

2019-11-06

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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