SMTL ID : 6lco.1

Crystal structure of bovine lactoperoxidase with substrates thiocynate and iodide bound at the distal heme side at 1.99 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: 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(Covalent)

HEM.2: 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, L.376, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: IOD.17, EDO.22, SCN.23 29 PLIP interactions: 28 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, 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:A.114, A:R.255, A:R.348, A:R.348, A:R.348, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.6

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 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

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

NAG.4: 6 residues within 4Å: Chain A: N.205, S.208, L.212, A.214, V.215, Q.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:Q.217 NAG.5: 2 residues within 4Å: Chain A: N.332, V.335 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.336 NAG.6: 5 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: SCN.26 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.96, A:Q.568 Water bridges: A:R.96, A:P.314, A:P.314

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

IOD.7: 4 residues within 4Å: Chain A: S.235, P.236, T.425 Ligands: SCN.27 Ligand excluded by PLIP IOD.8: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: E.77, N.80, P.145 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: R.202 Ligands: SCN.25 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: E.363, I.559, T.560, K.561 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: H.377 Ligands: SCN.24 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: H.565, A.566, F.567 Ligands: SCN.28 Ligand excluded by PLIP IOD.17: 5 residues within 4Å: Chain A: R.255, E.258 Ligands: HEM.2, EDO.22, SCN.23 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: F.254, R.255, F.381 Ligands: EDO.22 Ligand excluded by PLIP IOD.19: 4 residues within 4Å: Chain A: R.96, R.504, R.506 Ligands: SCN.26 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Chain A: W.46 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP IOD.33: 1 residues within 4Å: Chain A: S.198 Ligand excluded by PLIP

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

EDO.22: 9 residues within 4Å: Chain A: E.258, F.381, F.422, Q.423, P.424 Ligands: HEM.2, IOD.17, IOD.18, SCN.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.423

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

SCN.23: 7 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: HEM.2, IOD.17, EDO.22 No protein-ligand interaction detected (PLIP) SCN.24: 3 residues within 4Å: Chain A: H.377, H.429 Ligands: IOD.14 No protein-ligand interaction detected (PLIP) SCN.25: 2 residues within 4Å: Chain A: S.198 Ligands: IOD.11 No protein-ligand interaction detected (PLIP) SCN.26: 5 residues within 4Å: Chain A: N.95, R.96, R.506 Ligands: NAG.6, IOD.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.95, A:R.506, A:R.506 SCN.27: 7 residues within 4Å: Chain A: P.234, S.235, P.236, F.239, P.424, T.425 Ligands: IOD.7 No protein-ligand interaction detected (PLIP) SCN.28: 6 residues within 4Å: Chain A: D.311, H.565, A.566, F.567, Q.568 Ligands: IOD.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.566 Water bridges: A:D.311, A:F.549 SCN.29: 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

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

OSM.30: 5 residues within 4Å: Chain A: N.230, S.235, P.236, C.248, F.254 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.254 OSM.31: 5 residues within 4Å: Chain A: S.359, L.361, P.367, E.373, K.402 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.402 OSM.32: 4 residues within 4Å: Chain A: T.357, E.373, L.374, P.375 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, V. et al., Crystal structure of bovine lactoperoxidase with substrates thiocynate and iodide bound at the distal heme side at 1.99 A resolution. To Be Published

Release Date

2019-12-04

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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