SMTL ID : 9m0i.1

Structure of the intermediate of lactoperoxidase formed with thiocynate and hydrogen peroxidase at 1.99 A resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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 HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 26 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, Q.423, L.433, I.436, R.440 Ligands: IOD.16, SCN.21, PEO.28 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:Q.259, 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:A.114 Water bridges: A:F.113, 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

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 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

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

NAG.4: 6 residues within 4Å: Chain A: N.205, S.208, L.212, A.214, V.215, Q.217 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.217 Hydrogen bonds: A:S.208, A:V.215, A:Q.217 NAG.5: 2 residues within 4Å: Chain A: N.332, V.335 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.336 NAG.6: 5 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: SCN.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96, A:Q.568

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

IOD.7: 3 residues within 4Å: Chain A: S.235, P.236, T.425 Ligand excluded by PLIP IOD.8: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: E.77, N.80, P.145 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: R.202 Ligands: SCN.23 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: H.377 Ligands: SCN.22 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain A: H.565, A.566, F.567 Ligands: SCN.25 Ligand excluded by PLIP IOD.16: 5 residues within 4Å: Chain A: R.255, E.258 Ligands: HEM.2, SCN.21, PEO.28 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain A: F.254, R.255, F.381 Ligands: SCN.21 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain A: R.96, R.506 Ligands: SCN.24 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain A: W.46 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: P.149, N.419 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain A: E.196, S.198 Ligand excluded by PLIP IOD.32: 5 residues within 4Å: Chain A: R.397, I.559, T.560, K.561 Ligands: GOL.30 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain A: S.359 Ligands: GOL.31 Ligand excluded by PLIP IOD.34: 2 residues within 4Å: Chain A: E.373, P.375 Ligand excluded by PLIP

7 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.21: 8 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: HEM.2, IOD.16, IOD.17, PEO.28 No protein-ligand interaction detected (PLIP) SCN.22: 2 residues within 4Å: Chain A: H.429 Ligands: IOD.13 No protein-ligand interaction detected (PLIP) SCN.23: 2 residues within 4Å: Chain A: S.198 Ligands: IOD.11 No protein-ligand interaction detected (PLIP) SCN.24: 5 residues within 4Å: Chain A: N.95, R.96, R.506 Ligands: NAG.6, IOD.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.95, A:R.506, A:R.506 SCN.25: 6 residues within 4Å: Chain A: D.311, H.565, A.566, F.567, Q.568 Ligands: IOD.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.567, A:Q.568 SCN.26: 3 residues within 4Å: Chain A: R.31, Y.331, N.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.333 Water bridges: A:Y.331 SCN.29: 5 residues within 4Å: Chain A: N.230, K.232, P.236, C.248, F.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.230 Water bridges: A:S.257

1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.28: 6 residues within 4Å: Chain A: Q.105, H.109, H.351 Ligands: HEM.2, IOD.16, SCN.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:R.255

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.30: 8 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, I.559, T.560, K.561 Ligands: IOD.32 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.365, A:Y.365, A:R.397, A:R.397, A:H.558, A:T.560, A:K.561 GOL.31: 8 residues within 4Å: Chain A: S.359, R.360, L.361, P.367, A.372, E.373, K.402 Ligands: IOD.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.359, A:K.402

Links

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Citation

Viswanathan, V. et al., Structure of the intermediate of lactoperoxidase formed with thiocynate and hydrogen peroxidase at 1.99 A resolution. To Be Published

Release Date

2025-03-26

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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