SMTL ID : 7ve3.1

Structure of the complex of sheep lactoperoxidase with hypoiodite 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: 23 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, L.376, F.380, L.417, L.433, I.436, R.440 Ligands: 61D.12 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:D.108, A:E.258, 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 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Water bridges: A:R.255 Salt bridges: A:R.255, A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.1

1 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:T.184, A:T.184, A:F.186, A:S.190

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

NAG.3: 3 residues within 4Å: Chain A: N.332, S.334, V.335 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.336 NAG.4: 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

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

IOD.5: 2 residues within 4Å: Chain A: N.95, R.96 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: R.202 Ligands: IOD.7 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: S.198, R.202 Ligands: IOD.6 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: H.565, A.566, F.567, Q.568 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: N.216, F.229 Ligand excluded by PLIP

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

SO4.11: 3 residues within 4Å: Chain A: H.377, T.378, H.429 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.377, A:H.429

11 x 61D: hypoiodous acid(Non-covalent)

61D.12: 5 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.1, 61D.13 No protein-ligand interaction detected (PLIP) 61D.13: 3 residues within 4Å: Chain A: E.258, F.381 Ligands: 61D.12 No protein-ligand interaction detected (PLIP) 61D.14: 6 residues within 4Å: Chain A: N.230, M.232, P.234, S.235, P.236, C.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.232 Water bridges: A:M.232 61D.15: 5 residues within 4Å: Chain A: P.236, F.239, P.424, T.425, H.426 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.425, A:H.426 61D.16: 2 residues within 4Å: Chain A: F.309, W.530 No protein-ligand interaction detected (PLIP) 61D.17: 6 residues within 4Å: Chain A: S.359, L.361, P.367, A.372, E.373, K.402 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.402, A:K.402 61D.18: 5 residues within 4Å: Chain A: R.397, H.558, I.559, T.560, K.561 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.397, A:T.560, A:K.561 61D.19: 4 residues within 4Å: Chain A: P.461, K.462, T.463, G.466 No protein-ligand interaction detected (PLIP) 61D.20: 2 residues within 4Å: Chain A: P.197, A.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.197 Water bridges: A:R.204 61D.21: 3 residues within 4Å: Chain A: E.196, P.197, S.198 No protein-ligand interaction detected (PLIP) 61D.22: 7 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, N.341, V.342, W.452 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.45, A:L.47, A:L.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Structural evidence of the oxidation of iodide ion into hyper-reactive hypoiodite ion by mammalian heme lactoperoxidase. Protein Sci. (2022)

Release Date

2021-09-22

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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