SMTL ID : 3bxi.1

Structure of the complex of bovine lactoperoxidase with its catalyzed product hypothiocyanate ion at 2.3A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

2 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 6 residues within 4Å: Chain A: N.95, I.315, R.504, H.565, Q.568 Ligands: NO3.10 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

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.2: 8 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217, W.220 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.217, A:Q.217, A:W.220 NAG-NAG.4: 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.5: 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 SCN: THIOCYANATE ION(Non-functional Binders)

SCN.6: 3 residues within 4Å: Chain A: S.198, L.199, R.202 No protein-ligand interaction detected (PLIP)

5 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 9 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, S.340, N.341, V.342, M.446, W.452 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.45, A:W.46, A:L.47, A:N.341, A:V.342 NO3.8: 5 residues within 4Å: Chain A: N.216, Q.217, E.218, P.228, F.229 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.217, A:E.218, A:F.229 Water bridges: A:V.215 NO3.9: 7 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, I.559, T.560, K.561 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.365, A:R.397, A:R.397, A:T.560, A:K.561 Water bridges: A:E.363 NO3.10: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG-NAG-MAN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:R.504, A:R.506, A:R.506 NO3.11: 7 residues within 4Å: Chain A: Q.305, I.306, F.309, R.310, W.529, W.530, E.531 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.305

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.12: 23 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, R.255, E.258, Y.312, 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: OSM.13 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:E.258, 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 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Water bridges: A:E.116, A:R.348, A:R.348, A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351, OSM.13

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

OSM.13: 4 residues within 4Å: Chain A: Q.105, H.109, R.255 Ligands: HEM.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Inhibition of lactoperoxidase by its own catalytic product: crystal structure of the hypothiocyanate-inhibited bovine lactoperoxidase at 2.3-A resolution. Biophys.J. (2009)

Release Date

2008-03-25

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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