SMTL ID : 5b72.1

Crystal structure of bovine lactoperoxidase with a broken covalent bond between Glu258 and heme moiety at 1.98 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 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: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.95 Water bridges: A:R.504, A:R.504 Salt bridges: A:R.96, A:R.506

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

OSM.3: 4 residues within 4Å: Chain A: T.23, I.24, T.25 Ligands: PGE.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.24, A:T.25

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

IOD.4: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: R.453, P.509 Ligands: IOD.6 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: S.459 Ligands: IOD.5 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: Q.217, F.229 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain A: E.363, R.397, T.560, K.561 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: PGE.8 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: S.359, L.361, P.367 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: Q.468, T.469 Ligand excluded by PLIP

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 4 residues within 4Å: Chain A: P.197, S.201, R.204 Ligands: OSM.3 No protein-ligand interaction detected (PLIP) PGE.8: 4 residues within 4Å: Chain A: S.459, Q.460, V.470 Ligands: IOD.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.459, A:Q.460

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

NAG.9: 4 residues within 4Å: Chain A: N.95, R.96, I.315 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 NAG.10: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.205, A:V.215, A:Q.217, A:Q.217 Water bridges: A:S.207, A:S.207 NAG.11: 3 residues within 4Å: Chain A: N.332, S.334, 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.12: 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.19: 20 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, 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 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, 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:A.114 Water bridges: A:R.255, A:R.348, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.2

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

2016-07-13

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase