SMTL ID : 5ff1.2 (1 other biounit)

Two way mode of binding of antithyroid drug methimazole to mammalian heme peroxidases: Structure of the complex of lactoperoxidase with methimazole at 1.97 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.217

2 x MMZ: 1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE(Non-covalent)

MMZ.2: 7 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258, L.262 Ligands: HEM.6, MMZ.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.255 MMZ.12: 7 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258, L.262 Ligands: MMZ.2, HEM.6 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: N.95, R.96, I.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:N.95 NAG.4: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.241, A:A.244 Water bridges: A:T.243, A:T.243 NAG.5: 3 residues within 4Å: Chain A: N.332, S.334, V.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332

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, 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: MMZ.2, MMZ.12 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:Q.259, A:F.347, 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:A.114 Water bridges: A:A.114, A:R.255, A:R.348, 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 CA: CALCIUM ION(Non-covalent)

CA.7: 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

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

NO3.8: 9 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, S.340, N.341, V.342, M.446, W.452 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.46, A:L.47, A:L.47, A:N.341, A:V.342 Water bridges: A:R.45 NO3.9: 5 residues within 4Å: Chain A: R.76, D.148, P.149, K.150, N.419 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.76, A:K.150, A:R.418, A:N.419 Water bridges: A:K.150, A:K.150 NO3.10: 5 residues within 4Å: Chain A: D.311, H.565, A.566, F.567, Q.568 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.311, A:H.565, A:A.566, A:F.567, A:Q.568 NO3.11: 3 residues within 4Å: Chain A: L.92, K.402, N.403 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.403 Water bridges: A:T.357, A:K.402, A:K.402, A:N.403

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 5 residues within 4Å: Chain A: A.56, V.57, W.61, D.137, R.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.56, A:D.137, A:E.138, A:R.162 GOL.14: 10 residues within 4Å: Chain A: E.52, P.58, F.59, G.60, W.61, T.62, K.65, T.66, R.71, V.72 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.52, A:G.60, A:W.61, A:T.62, A:R.71, A:V.72 GOL.15: 4 residues within 4Å: Chain A: E.52, F.59, K.65, T.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.52, A:T.66 Water bridges: A:N.68 GOL.16: 5 residues within 4Å: Chain A: R.527, N.532, P.533, G.534, V.535 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.527 Water bridges: A:N.532, A:N.532

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R.P. et al., Dual binding mode of antithyroid drug methimazole to mammalian heme peroxidases - structural determination of the lactoperoxidase-methimazole complex at 1.97 angstrom resolution. Febs Open Bio (2016)

Release Date

2016-01-13

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Lactoperoxidase

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