SMTL ID : 5hpw.3 (3 other biounits)

Mode of binding of antithyroid drug, propylthiouracil to lactoperoxidase: Binding studies and structure determination

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: 5 residues within 4Å: Chain A: I.240, N.241, T.243, A.244, W.384 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: N.95, I.315, Q.568 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.95 NAG.3: 7 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.214 Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:N.205

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: D.110, L.111, 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:T.184, A:F.186

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

NO3.5: 6 residues within 4Å: Chain A: Q.305, F.309, R.310, W.529, W.530, E.531 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.530 NO3.6: 4 residues within 4Å: Chain A: L.92, A.401, K.402, N.403 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.403 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.44, A:R.45, A:W.46, A:L.47, A:N.341, A:V.342

1 x 3CJ: 6-propyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one(Non-covalent)

3CJ.8: 9 residues within 4Å: Chain A: Q.105, D.108, H.109, F.113, A.114, R.255, E.258, R.348 Ligands: HEM.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.113, A:R.255 Hydrogen bonds: A:Q.105, A:R.255

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.9: 21 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, E.258, Q.259, Y.312, T.344, F.347, R.348, G.350, H.351, V.354, L.417, L.433, I.436, R.440 Ligands: 3CJ.8 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Q.105, A:E.258, A:Q.259, A:F.347, A:F.347, A:R.348, A:V.354, A:V.354, A:L.417, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:A.114 Salt bridges: A:R.348, A:R.440 pi-Stacking: A:H.351 Metal complexes: A:H.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R.P. et al., Mode of binding of antithyroid drug, propylthiouracil to lactoperoxidase: Binding studies and structure determination. To Be Published

Release Date

2016-04-20

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Lactoperoxidase

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