SMTL ID : 5zgs.1

Crystal structure of the complex of bovine lactoperoxidase with multiple SCN and OSCN ions in the distal heme cavity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 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, L.376, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: IOD.22, OSM.25 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:Q.259, 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:F.113, A:R.255, 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)

NAG.3: 4 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 Water bridges: A:N.95 NAG.4: 7 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.217 Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:N.205, A:N.205 NAG.5: 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

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 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

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

SCN.7: 4 residues within 4Å: Chain A: S.459, P.461, G.466 Ligands: IOD.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.459 SCN.8: 2 residues within 4Å: Chain A: S.198, R.202 No protein-ligand interaction detected (PLIP) SCN.9: 3 residues within 4Å: Chain A: P.197, A.200, S.201 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.204 SCN.10: 4 residues within 4Å: Chain A: N.230, P.236, C.248, F.381 No protein-ligand interaction detected (PLIP) SCN.11: 6 residues within 4Å: Chain A: F.254, R.255, E.258, F.381 Ligands: IOD.22, OSM.25 No protein-ligand interaction detected (PLIP)

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

IOD.12: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: SCN.7 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.16: 5 residues within 4Å: Chain A: E.363, R.397, I.559, T.560, K.561 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: A.225, R.271 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain A: R.31, Y.331, N.333 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.22: 5 residues within 4Å: Chain A: R.255, E.258 Ligands: HEM.2, SCN.11, OSM.25 Ligand excluded by PLIP

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

PEG.23: 7 residues within 4Å: Chain A: R.32, S.33, L.36, S.334, V.335, D.336, R.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.32, A:S.33

1 x NA: SODIUM ION(Non-functional Binders)

NA.24: 1 residues within 4Å: Chain A: E.538 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.538

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

OSM.25: 6 residues within 4Å: Chain A: Q.105, H.109, R.255 Ligands: HEM.2, SCN.11, IOD.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Crystal structure of the complex of bovine lactoperoxidase with multiple SCN and OSCN ions in the distal heme cavity. To Be Published

Release Date

2018-05-23

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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