SMTL ID : 7dn6.1

Crystal structure of bovine lactoperoxidase with hydrogen peroxide trapped between heme iron and his109 at 1.69 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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: 3 residues within 4Å: Chain A: N.241, A.244, W.384 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 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, T.344, F.347, R.348, G.350, H.351, V.354, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: IOD.21, PEO.28 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:E.258, A:Q.259, A:F.347, A:F.347, A:R.348, A:V.354, A:V.354, A:F.380, A:L.417, A:L.433, 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.348, A:R.440 Metal complexes: A:H.351

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 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

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

NAG.4: 2 residues within 4Å: Chain A: N.332, V.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:N.332 NAG.31: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.205, A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:N.205, A:S.207

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

IOD.5: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: R.96 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: F.229, I.387 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: A.225 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: S.359, L.361, P.367 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: R.31, N.333 Ligands: OSM.20 Ligand excluded by PLIP IOD.21: 5 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.2, PEO.28 Ligand excluded by PLIP IOD.22: 1 residues within 4Å: Chain A: P.197 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain A: F.254, F.381 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain A: L.86, D.87 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: L.199, R.202 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: P.197, S.198 Ligand excluded by PLIP IOD.27: 4 residues within 4Å: Chain A: E.363, R.397, T.560, K.561 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.30: 1 residues within 4Å: Chain A: T.66 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 3 residues within 4Å: Chain A: H.377, T.378, H.429 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.429 Water bridges: A:H.429, A:H.429

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.16: 2 residues within 4Å: Chain A: D.362, E.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.363, A:E.363, A:E.363

1 x ZN: ZINC ION(Non-covalent)

ZN.17: 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

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

OSM.18: 5 residues within 4Å: Chain A: N.230, K.232, S.235, P.236, C.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.230 Water bridges: A:F.254 OSM.19: 4 residues within 4Å: Chain A: R.76, P.149, K.150, N.419 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.150, A:N.419 Water bridges: A:P.149, A:R.418, A:N.419 OSM.20: 5 residues within 4Å: Chain A: R.31, Y.331, N.333, R.527 Ligands: IOD.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.31, A:R.527 Water bridges: A:R.31, A:Y.331

1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.28: 4 residues within 4Å: Chain A: Q.105, H.109 Ligands: HEM.2, IOD.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.105, A:H.109 Water bridges: A:R.255, A:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Structure of a ternary complex of lactoperoxidase with iodide and hydrogen peroxide at 1.77 angstrom resolution. J.Inorg.Biochem. (2021)

Release Date

2020-12-30

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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