SMTL ID : 3faq.1

Crystal structure of lactoperoxidase complex with cyanide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 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: 4 residues within 4Å: Chain A: N.95, R.504, H.565 Ligands: IOD.11 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.217

1 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(Non-functional Binders)

NAG-NAG-MAN.3: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN.4: 2 residues within 4Å: Chain A: N.332, V.335 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 23 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, Q.423, L.433, I.436, R.440 Ligands: SCN.7, CYN.9 20 PLIP interactions: 20 interactions with chain A, 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:F.380, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:A.114 Water bridges: A:R.348, A:R.348, A:R.440 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

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

SCN.6: 2 residues within 4Å: Chain A: S.198, R.202 No protein-ligand interaction detected (PLIP) SCN.7: 4 residues within 4Å: Chain A: R.255, E.258 Ligands: HEM.5, CYN.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.423

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 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 CYN: CYANIDE ION(Non-covalent)

CYN.9: 4 residues within 4Å: Chain A: Q.105, H.109 Ligands: HEM.5, SCN.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.105

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

IOD.10: 3 residues within 4Å: Chain A: E.77, N.80, P.145 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: R.96, R.504 Ligands: NAG-NAG.1 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain A: W.530 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP IOD.15: 5 residues within 4Å: Chain A: R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sheikh, I.A. et al., Structural Evidence of Substrate Specificity in Mammalian Peroxidases: STRUCTURE OF THE THIOCYANATE COMPLEX WITH LACTOPEROXIDASE AND ITS INTERACTIONS AT 2.4 A RESOLUTION. J.Biol.Chem. (2009)

Release Date

2009-03-31

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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