SMTL ID : 6l9e.1

Crystal structure of bovine lactoperoxidase with hydrogen peroxide trapped between heme iron and his109 at 1.69 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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(Non-covalent)

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 CA: CALCIUM ION(Covalent)

CA.2: 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 HEM: PROTOPORPHYRIN IX CONTAINING FE(Post Translational Modification)

HEM.3: 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, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: IOD.26, PEO.31, PEO.32, SCN.33 28 PLIP interactions: 28 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: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

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

NAG.4: 3 residues within 4Å: Chain A: N.95, R.96, I.315 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 Water bridges: A:N.95, A:R.96 NAG.5: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.217 Hydrogen bonds: A:N.205, A:S.208, A:V.215, A:Q.217, A:Q.217 NAG.6: 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

17 x IOD: IODIDE ION(Post Translational Modification)(Non-functional Binders)

IOD.7: 7 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligands: SCN.34 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: 1 residues within 4Å: Chain A: R.96 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: F.309, W.530 Ligands: SCN.36 Ligand excluded by PLIP IOD.11: 6 residues within 4Å: Chain A: E.363, R.397, I.559, T.560, K.561 Ligands: SCN.37 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: F.229, I.387 Ligands: SCN.38 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: A.225 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: S.359, L.361, P.367 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: P.236, T.425 Ligands: SCN.39 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: SCN.40 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligands: SCN.41 Ligand excluded by PLIP IOD.26: 7 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.3, PEO.31, PEO.32, SCN.33 Ligand excluded by PLIP IOD.27: 5 residues within 4Å: Chain A: F.254, R.255, F.381 Ligands: PEO.31, SCN.33 Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain A: P.197 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain A: L.199, R.202 Ligand excluded by PLIP IOD.30: 1 residues within 4Å: Chain A: E.373 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-functional Binders)

ZN.19: 2 residues within 4Å: Chain A: H.222, H.558 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.222, A:H.558

1 x GOL: GLYCEROL(Non-covalent)

GOL.20: 7 residues within 4Å: Chain A: N.30, R.32, L.36, N.333, S.334, V.335, D.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.30, A:N.333 Water bridges: A:S.33

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

SCN.21: 3 residues within 4Å: Chain A: N.230, P.236, C.248 No protein-ligand interaction detected (PLIP) SCN.33: 9 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: HEM.3, IOD.26, IOD.27, PEO.31, PEO.32 No protein-ligand interaction detected (PLIP) SCN.34: 10 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, S.340, N.341, V.342, M.446, W.452 Ligands: IOD.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.45, A:V.342 SCN.35: 6 residues within 4Å: Chain A: N.80, K.81, P.145, N.147, D.148 Ligands: IOD.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.80, A:D.148 Water bridges: A:N.147 SCN.36: 5 residues within 4Å: Chain A: I.306, F.309, R.310, W.530 Ligands: IOD.10 No protein-ligand interaction detected (PLIP) SCN.37: 6 residues within 4Å: Chain A: E.363, Y.365, R.397, T.560, K.561 Ligands: IOD.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.560, A:K.561 SCN.38: 7 residues within 4Å: Chain A: E.218, A.219, F.229, R.245, V.246, I.387 Ligands: IOD.13 No protein-ligand interaction detected (PLIP) SCN.39: 7 residues within 4Å: Chain A: S.235, P.236, F.239, F.422, T.425, H.426 Ligands: IOD.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.425 SCN.40: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: IOD.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.462, A:T.463 SCN.41: 7 residues within 4Å: Chain A: V.215, N.216, Q.217, P.228, F.229, N.231 Ligands: IOD.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.229, A:F.229

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

PEG.22: 6 residues within 4Å: Chain A: R.76, N.80, P.149, K.150, R.418, N.419 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.76, A:N.80, A:K.150, A:R.418 Water bridges: A:K.150, A:T.153, A:T.153, A:Q.154 PEG.23: 4 residues within 4Å: Chain A: R.45, W.46, L.47, P.48 No protein-ligand interaction detected (PLIP)

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

EDO.24: 3 residues within 4Å: Chain A: H.377, T.378, H.429 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.377 Water bridges: A:I.240 EDO.25: 5 residues within 4Å: Chain A: S.33, A.35, L.36, R.41, R.338 6 PLIP interactions: 6 interactions with chain A Water bridges: A:S.33, A:S.33, A:A.35, A:A.35, A:G.37, A:R.338

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

PEO.31: 8 residues within 4Å: Chain A: E.258, F.381, Q.423, P.424 Ligands: HEM.3, IOD.26, IOD.27, SCN.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.423 PEO.32: 5 residues within 4Å: Chain A: Q.105, H.109 Ligands: HEM.3, IOD.26, SCN.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:R.255, A:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Crystal structure of bovine lactoperoxidase with hydrogen peroxide trapped between heme iron and his109 at 1.69 A resolution. To Be Published

Release Date

2019-11-20

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

Related Entries With Identical Sequence