SMTL ID : 5zww.1

CRYSTAL STRUCTURE OF THE COMPLEX OF LACTOPEROXIDASE WITH HYDROGEN PEROXIDE AT 1.77A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Covalent)(Non-covalent)

NAG-NAG.1: 6 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217, W.220 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 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(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.28, PEO.35, PEO.36, PEO.37 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: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: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

1 x CA: CALCIUM ION(Non-covalent)

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

NAG.5: 3 residues within 4Å: Chain A: N.332, S.334, V.335 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.332, A:N.332, A:S.334, A:D.336, A:D.336

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

IOD.6: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: R.96 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: F.229, I.387 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: A.225, R.271 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain A: S.359, L.361, P.367, K.402 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: P.236, T.425 Ligands: OSM.22 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: K.462, T.463 Ligands: OSM.23 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: R.31, N.333 Ligands: OSM.25 Ligand excluded by PLIP IOD.28: 7 residues within 4Å: Chain A: R.255, E.258 Ligands: HEM.3, PEO.35, PEO.36, PEO.37, PEO.38 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain A: P.197 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain A: F.254, F.381 Ligands: PEO.37, PEO.38 Ligand excluded by PLIP IOD.31: 3 residues within 4Å: Chain A: Y.85, L.86, D.87 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain A: L.199, R.202 Ligands: OSM.26 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain A: P.197, S.198 Ligand excluded by PLIP IOD.34: 6 residues within 4Å: Chain A: E.363, R.397, I.559, T.560, K.561 Ligands: OSM.27 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 3 residues within 4Å: Chain A: H.377, T.378, H.429 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.429 Water bridges: A:T.378, A:H.429

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

EDO.19: 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 ZN: ZINC ION(Non-functional Binders)

ZN.20: 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

7 x OSM: 1-(OXIDOSULFANYL)METHANAMINE(Non-functional Binders)(Non-covalent)

OSM.21: 4 residues within 4Å: Chain A: N.230, S.235, P.236, C.248 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.254 OSM.22: 8 residues within 4Å: Chain A: P.234, S.235, P.236, F.239, F.422, P.424, T.425 Ligands: IOD.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.425 OSM.23: 5 residues within 4Å: Chain A: P.461, K.462, T.463, G.466 Ligands: IOD.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.462, A:T.463, A:G.466 OSM.24: 3 residues within 4Å: Chain A: R.76, P.149, N.419 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.76, A:N.419 Water bridges: A:P.149, A:K.150, A:K.150 OSM.25: 5 residues within 4Å: Chain A: R.31, Y.331, N.333, R.527 Ligands: IOD.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.31, A:R.31, A:N.333 Water bridges: A:Y.331 OSM.26: 4 residues within 4Å: Chain A: S.198, L.199, R.202 Ligands: IOD.32 No protein-ligand interaction detected (PLIP) OSM.27: 8 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, I.559, T.560, K.561 Ligands: IOD.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.397, A:T.560, A:K.561

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

PEO.35: 5 residues within 4Å: Chain A: Q.105, H.109 Ligands: HEM.3, IOD.28, PEO.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.105, A:H.109, A:R.255 PEO.36: 6 residues within 4Å: Chain A: H.109, F.113, R.255 Ligands: HEM.3, IOD.28, PEO.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.109, A:R.255 PEO.37: 8 residues within 4Å: Chain A: E.258, F.381, Q.423, P.424 Ligands: HEM.3, IOD.28, IOD.30, PEO.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.423 PEO.38: 6 residues within 4Å: Chain A: R.255, E.258, F.381 Ligands: IOD.28, IOD.30, PEO.37 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., CRYSTAL STRUCTURE OF THE COMPLEX OF LACTOPEROXIDASE WITH HYDROGEN PEROXIDE AT 1.77A RESOLUTION. To Be Published

Release Date

2018-06-13

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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