SMTL ID : 6lf7.1

Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite and hydrogen peroxide at 1.79 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.95, R.96, I.315 Ligands: OSM.26, OSM.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 NAG.2: 6 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.205, A:S.208, A:V.215, A:Q.217 NAG.3: 3 residues within 4Å: Chain A: N.241, A.244, W.384 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 25 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: PEO.18, OSM.22 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:Q.105, 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.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.440 Metal complexes: A:H.351

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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

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

IOD.6: 7 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligands: SCN.31 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligands: SCN.36 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: N.80, P.145 Ligands: SCN.35 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: P.236, F.239, T.425 Ligands: SCN.30 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: R.31, Y.331, N.333 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: W.46, P.48 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: L.86, D.87 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: E.363, R.397, T.560 Ligands: SCN.34 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: F.309, W.530 Ligands: SCN.33 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain A: T.66 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: S.198 Ligands: SCN.32 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: Q.409, N.410, N.473 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 4 residues within 4Å: Chain A: A.35, L.36, R.41, R.338 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.37, A:A.42, A:A.42 EDO.12: 4 residues within 4Å: Chain A: I.24, P.197, A.200, S.201 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.24 EDO.13: 6 residues within 4Å: Chain A: S.359, L.361, P.367, A.372, E.373, K.402 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.402 EDO.37: 6 residues within 4Å: Chain A: L.224, A.225, R.271, N.274, R.275, R.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.225, A:R.271, A:R.275, A:R.278 Water bridges: A:G.223

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

PEO.18: 4 residues within 4Å: Chain A: Q.105, H.109 Ligands: HEM.4, OSM.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105, A:H.351

8 x OSM: 1-(OXIDOSULFANYL)METHANAMINE(Non-covalent)

OSM.22: 6 residues within 4Å: Chain A: H.109, R.255, E.258, F.381 Ligands: HEM.4, PEO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:R.255 OSM.23: 1 residues within 4Å: Chain A: L.12 No protein-ligand interaction detected (PLIP) OSM.24: 3 residues within 4Å: Chain A: H.377, T.378, H.429 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.377 OSM.25: 1 residues within 4Å: Chain A: R.541 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.541 OSM.26: 6 residues within 4Å: Chain A: D.311, H.565, A.566, F.567, Q.568 Ligands: NAG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.566 Water bridges: A:R.310, A:F.549 OSM.27: 4 residues within 4Å: Chain A: R.76, P.149, K.150, N.419 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.150 Water bridges: A:P.149, A:R.418 OSM.28: 5 residues within 4Å: Chain A: E.218, A.219, F.229, H.245, V.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.218 OSM.29: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:R.506

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

SCN.30: 6 residues within 4Å: Chain A: P.234, S.235, P.236, P.424, T.425 Ligands: IOD.9 No protein-ligand interaction detected (PLIP) SCN.31: 9 residues within 4Å: Chain A: A.44, R.45, W.46, S.340, N.341, V.342, M.446, W.452 Ligands: IOD.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.45, A:V.342 SCN.32: 4 residues within 4Å: Chain A: E.196, P.197, S.198 Ligands: IOD.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.198 SCN.33: 5 residues within 4Å: Chain A: Q.305, I.306, F.309, W.530 Ligands: IOD.17 No protein-ligand interaction detected (PLIP) SCN.34: 8 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, V.559, T.560, K.561 Ligands: IOD.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.560, A:K.561 SCN.35: 8 residues within 4Å: Chain A: E.77, N.80, K.81, P.145, K.146, N.147, D.148 Ligands: IOD.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 SCN.36: 6 residues within 4Å: Chain A: V.215, N.216, Q.217, P.228, F.229 Ligands: IOD.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217, A:F.229

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.38: 3 residues within 4Å: Chain A: S.198, L.199, R.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, V. et al., Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite and hydrogen peroxide at 1.79 A resolution. To Be Published

Release Date

2020-01-22

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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