SMTL ID : 6laq.1

Crystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide, SCN, and iodide at 1.70 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 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 ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.222, H.558 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.222, A:H.558, H2O.19

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 27 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: PEO.21, PEO.22, PEO.23, IOD.24, SCN.41 27 PLIP interactions: 27 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: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:F.113, A:E.116, A:R.255, A:R.348, A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

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

NAG.4: 6 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: IOD.10, SCN.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 NAG.5: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Q.217 Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:N.205, A:S.207, A:S.207 NAG.6: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.241 NAG.7: 3 residues within 4Å: Chain A: N.332, S.334, V.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:N.332, A:D.524

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

IOD.8: 7 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligands: SCN.42 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.80, P.145 Ligands: SCN.34 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: N.95, R.96 Ligands: NAG.4, SCN.38 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: SCN.39 Ligand excluded by PLIP IOD.13: 5 residues within 4Å: Chain A: N.216, Q.217, E.218, F.229 Ligands: SCN.33 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: P.236, T.425 Ligands: SCN.32 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Ligands: SCN.40 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: A.225 Ligand excluded by PLIP IOD.24: 7 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.3, PEO.21, PEO.22, SCN.41 Ligand excluded by PLIP IOD.25: 4 residues within 4Å: Chain A: R.255, F.381 Ligands: PEO.22, SCN.41 Ligand excluded by PLIP IOD.26: 1 residues within 4Å: Chain A: P.197 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain A: L.199, R.202 Ligands: SCN.37 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain A: P.197, S.198 Ligands: SCN.36 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain A: E.363, R.397, T.560 Ligands: SCN.43 Ligand excluded by PLIP IOD.31: 1 residues within 4Å: Chain A: T.66 Ligand excluded by PLIP

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

SCN.18: 2 residues within 4Å: Chain A: P.236, C.248 No protein-ligand interaction detected (PLIP) SCN.32: 7 residues within 4Å: Chain A: S.235, P.236, F.239, F.422, T.425, H.426 Ligands: IOD.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.425 SCN.33: 6 residues within 4Å: Chain A: N.216, Q.217, E.218, F.229, N.231 Ligands: IOD.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.229 SCN.34: 7 residues within 4Å: Chain A: E.77, N.80, K.81, P.145, N.147, D.148 Ligands: IOD.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.80, A:N.147 SCN.35: 3 residues within 4Å: Chain A: R.31, Y.331, N.333 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.333 SCN.36: 4 residues within 4Å: Chain A: E.196, P.197, S.198 Ligands: IOD.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.198 SCN.37: 2 residues within 4Å: Chain A: S.198 Ligands: IOD.27 No protein-ligand interaction detected (PLIP) SCN.38: 5 residues within 4Å: Chain A: R.96, R.504, R.506 Ligands: NAG.4, IOD.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.506, A:R.506 SCN.39: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: IOD.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.462, A:T.463, A:G.466 SCN.40: 6 residues within 4Å: Chain A: F.229, R.245, V.246, P.247, I.387 Ligands: IOD.16 No protein-ligand interaction detected (PLIP) SCN.41: 9 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: HEM.3, PEO.21, PEO.22, IOD.24, IOD.25 No protein-ligand interaction detected (PLIP) SCN.42: 9 residues within 4Å: Chain A: A.44, R.45, W.46, S.340, N.341, V.342, M.446, W.452 Ligands: IOD.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.45, A:N.341, A:N.341 SCN.43: 8 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, I.559, T.560, K.561 Ligands: IOD.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.397, A:H.558, A:T.560 SCN.44: 4 residues within 4Å: Chain A: S.359, L.361, P.367, K.402 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.402

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

EDO.19: 3 residues within 4Å: Chain A: H.377, T.378, H.429 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.378, A:H.429 EDO.45: 2 residues within 4Å: Chain A: D.362, E.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.363, A:E.363, A:E.363

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.20: 4 residues within 4Å: Chain A: R.45, W.46, L.47, P.48 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.178

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

PEO.21: 5 residues within 4Å: Chain A: Q.105, H.109 Ligands: HEM.3, IOD.24, SCN.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.105, A:H.109 Water bridges: A:R.255 PEO.22: 7 residues within 4Å: Chain A: E.258, F.381, Q.423 Ligands: HEM.3, IOD.24, IOD.25, SCN.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.423 PEO.23: 3 residues within 4Å: Chain A: A.114, R.440 Ligands: HEM.3 5 PLIP interactions: 5 interactions with chain A Water bridges: A:A.114, A:A.114, A:E.116, A:E.116, A:R.348

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Crystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide, SCN, and iodide at 1.70 A resolution. To Be Published

Release Date

2019-12-25

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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