SMTL ID : 6l9t.1

Crystal structure of the complex of bovine lactoperoxidase with OSCN at 1.89 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 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(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217, A:Q.217 NAG-NAG.2: 3 residues within 4Å: Chain A: N.332, S.334, V.335 No protein-ligand interaction detected (PLIP)

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

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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 HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 25 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.25, SCN.35, OSM.36 32 PLIP interactions: 31 interactions with chain A, 1 Ligand-Ligand interactions 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, A:R.348, A:Q.423, A:Q.423, A:R.440 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, OSM.36

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

NAG.6: 6 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: SCN.28, SCN.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:N.95 NAG.7: 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 Water bridges: A:R.385

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

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: 3 residues within 4Å: Chain A: R.96, R.506 Ligands: SCN.28 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: E.218, F.229, N.231 Ligands: SCN.27 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: S.33, P.34, A.35 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain A: E.363, Y.365, R.397 Ligands: SCN.29 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Ligands: SCN.30 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: H.565, A.566, F.567 Ligands: SCN.31 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: S.359, K.402 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: S.198 Ligands: SCN.32 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain A: R.31 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: H.377 Ligands: SCN.33 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain A: P.375 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP IOD.23: 4 residues within 4Å: Chain A: K.150, N.419, H.429, G.430 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.25: 6 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.5, SCN.35, OSM.36 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain A: L.199, R.202 Ligands: SCN.34 Ligand excluded by PLIP

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

SCN.27: 6 residues within 4Å: Chain A: V.215, N.216, Q.217, F.229, N.231 Ligands: IOD.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.229 SCN.28: 6 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG.6, IOD.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.506 Water bridges: A:R.506 SCN.29: 8 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, I.559, T.560, K.561 Ligands: IOD.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.365, A:T.560, A:K.561 SCN.30: 2 residues within 4Å: Chain A: P.11 Ligands: IOD.15 No protein-ligand interaction detected (PLIP) SCN.31: 6 residues within 4Å: Chain A: D.311, H.565, A.566, F.567 Ligands: NAG.6, IOD.16 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.566, A:F.567 Water bridges: A:R.310, A:D.311, A:F.549 SCN.32: 4 residues within 4Å: Chain A: E.196, P.197, S.198 Ligands: IOD.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.198 SCN.33: 4 residues within 4Å: Chain A: H.377, T.378, H.429 Ligands: IOD.20 No protein-ligand interaction detected (PLIP) SCN.34: 3 residues within 4Å: Chain A: S.198, R.202 Ligands: IOD.26 No protein-ligand interaction detected (PLIP) SCN.35: 7 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: HEM.5, IOD.25, OSM.36 No protein-ligand interaction detected (PLIP)

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

OSM.36: 7 residues within 4Å: Chain A: Q.105, D.108, H.109, R.255 Ligands: HEM.5, IOD.25, SCN.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.105, A:D.108, A:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Crystal structure of the complex of bovine lactoperoxidase with OSCN at 1.89 A resolution. To Be Published

Release Date

2020-09-16

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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