SMTL ID : 3krq.1

Crystal structure of the complex of lactoperoxidase with a potent inhibitor amino-triazole at 2.2a resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 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(Covalent)

NAG-NAG-MAN.1: 6 residues within 4Å: Chain A: N.95, R.96, P.314, I.315, R.504 Ligands: IOD.13 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 5 residues within 4Å: Chain A: N.241, A.244, W.384, K.388, D.389 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.389

1 x NAG- NAG- BMA: 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.2: 7 residues within 4Å: Chain A: N.205, S.208, L.212, A.214, V.215, Q.217, W.220 No protein-ligand interaction detected (PLIP)

1 x NAG- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG.4: 3 residues within 4Å: Chain A: N.332, S.334, V.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332, A:S.334

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 22 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, L.433, I.436, R.440 Ligands: 3TR.14 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:E.258, A:Q.259, A:F.347, A:F.347, A:R.348, 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:R.348, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

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:T.184, A:T.184, A:F.186, A:S.190

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

IOD.7: 5 residues within 4Å: Chain A: R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: P.234, P.236, F.239, P.424 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: N.95, R.506 Ligands: NAG-NAG-MAN.1 Ligand excluded by PLIP

2 x 3TR: 3-AMINO-1,2,4-TRIAZOLE(Non-covalent)

3TR.14: 6 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: HEM.5, 3TR.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:R.255 Salt bridges: A:E.258 pi-Cation interactions: A:R.255 3TR.15: 5 residues within 4Å: Chain A: F.254, R.255, F.381, P.424 Ligands: 3TR.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.254 Water bridges: A:E.258 pi-Stacking: A:F.381

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.16: 4 residues within 4Å: Chain A: R.31, Y.331, N.333, R.527 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.331 Hydrogen bonds: A:R.31, A:N.333

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

PEG.17: 1 residues within 4Å: Chain A: K.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., First structural evidence for the mode of diffusion of aromatic ligands and ligand-induced closure of the hydrophobic channel in heme peroxidases. J.Biol.Inorg.Chem. (2010)

Release Date

2010-05-26

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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