SMTL ID : 6a4y.1

Crystal structure of bovine lactoperoxidase with partial occupancies of iodide and SCN- ions at the substrate binding site on the distal heme side at 1.92 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 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: 3 residues within 4Å: Chain A: N.205, S.208, V.215 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 24 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, L.433, I.436, R.440 Ligands: IOD.6, SCN.18 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions 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:D.112, A:A.114 Water bridges: A:R.348, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.4

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

NAG.3: 2 residues within 4Å: Chain A: N.95, Q.568 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.241, A:K.388 NAG.5: 1 residues within 4Å: Chain A: N.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332

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

IOD.6: 5 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.2, SCN.18 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: W.530 Ligands: SCN.15 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: P.236, P.424 Ligands: SCN.17 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: L.86, D.87, K.411 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: K.462, T.463 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 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:T.184, A:T.184, A:F.186, A:S.190

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

SCN.11: 5 residues within 4Å: Chain A: C.248, F.254, A.256, S.257, F.381 No protein-ligand interaction detected (PLIP) SCN.12: 3 residues within 4Å: Chain A: H.377, T.378, H.429 No protein-ligand interaction detected (PLIP) SCN.13: 3 residues within 4Å: Chain A: R.76, P.149, N.419 No protein-ligand interaction detected (PLIP) SCN.14: 4 residues within 4Å: Chain A: S.359, P.367, E.373, K.402 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.359, A:K.402 SCN.15: 6 residues within 4Å: Chain A: Q.305, I.306, F.309, W.529, W.530 Ligands: IOD.8 No protein-ligand interaction detected (PLIP) SCN.16: 10 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, P.48, N.341, V.342, M.446, P.447, W.452 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.45 SCN.17: 7 residues within 4Å: Chain A: S.235, P.236, F.239, F.422, P.424, H.426 Ligands: IOD.9 No protein-ligand interaction detected (PLIP) SCN.18: 5 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.2, IOD.6 No protein-ligand interaction detected (PLIP)

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

OSM.21: 4 residues within 4Å: Chain A: S.198, L.199, R.202, K.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.202, A:K.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Crystal structure of bovine lactoperoxidase with partial occupancies of iodide and SCN- ions at the substrate binding site on the distal heme side at 1.92 A resolution. To Be Published

Release Date

2018-07-04

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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