SMTL ID : 5gh0.1

Crystal structure of the complex of bovine lactoperoxidase with mercaptoimidazole at 2.3 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217 Water bridges: A:Q.217

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 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, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: MZY.10 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:E.258, A:Q.259, 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.348, A:R.348, A:R.440 Metal complexes: A:H.351

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

NAG.3: 5 residues within 4Å: Chain A: N.95, I.315, R.504, Q.568 Ligands: CO3.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.96, A:R.504 Water bridges: A:R.96, A:R.504 NAG.4: 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.5: 2 residues within 4Å: Chain A: N.332, V.335 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.332

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.6: 6 residues within 4Å: Chain A: E.363, Y.365, R.397, I.559, T.560, K.561 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.397, A:H.558, A:T.560, A:K.561 Water bridges: A:E.363 NO3.7: 9 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, S.340, N.341, V.342, M.446, W.452 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.45, A:W.46, A:L.47, A:N.341, A:V.342

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.8: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:R.504

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 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 MZY: 1,3-dihydroimidazole-2-thione(Non-covalent)

MZY.10: 5 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: HEM.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105, A:E.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sirohi, H.V. et al., Design of anti-thyroid drugs: Binding studies and structure determination of the complex of lactoperoxidase with 2-mercaptoimidazole at 2.30 angstrom resolution. Proteins (2017)

Release Date

2016-06-29

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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