SMTL ID : 5gls.1

Structure of bovine Lactoperoxidase with a partially modified covalent bond with heme moiety

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 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)

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

NAG.2: 5 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: SCN.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 NAG.3: 6 residues within 4Å: Chain A: N.205, S.208, M.213, 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, V.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332, 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(Covalent)

HEM.6: 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, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: IOD.8 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.259, A:F.347, A:F.347, A:R.348, A:V.354, A:F.380, A:L.417, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:A.114 Water bridges: A:R.255, A:R.255, A:R.348, A:R.348, A:R.348, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.7: 3 residues within 4Å: Chain A: R.96, R.506 Ligands: NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96, A:R.96

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

IOD.8: 3 residues within 4Å: Chain A: Q.105, H.109 Ligands: HEM.6 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: F.309, W.530 Ligands: IOD.10 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: F.309 Ligands: IOD.9 Ligand excluded by PLIP IOD.11: 7 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligands: IOD.14 Ligand excluded by PLIP IOD.12: 5 residues within 4Å: Chain A: E.77, N.80, K.81, P.145 Ligands: IOD.13 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: N.80, P.145 Ligands: IOD.12 Ligand excluded by PLIP IOD.14: 7 residues within 4Å: Chain A: R.45, W.46, N.341, V.342, M.446, W.452 Ligands: IOD.11 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: R.31, N.333 Ligands: IOD.19 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain A: T.66 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: P.197 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain A: S.359, L.361, K.402 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: Y.331, N.333 Ligands: IOD.15 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain A: K.462, T.463 Ligands: IOD.21 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: K.462, G.466 Ligands: IOD.20 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain A: H.377, H.429 Ligand excluded by PLIP IOD.23: 4 residues within 4Å: Chain A: S.235, P.236, T.425 Ligands: IOD.24 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain A: T.425 Ligands: IOD.23 Ligand excluded by PLIP IOD.25: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP

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

OSM.26: 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:E.363, A:R.397, A:T.560, A:K.561 OSM.27: 5 residues within 4Å: Chain A: V.215, N.216, Q.217, E.218, F.229 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.215, A:Q.217, A:E.218, A:E.218, A:F.229

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Structure of bovine lactoperoxidase with a partially linked heme moiety at 1.98 angstrom resolution. Biochim. Biophys. Acta (2016)

Release Date

2016-07-27

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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