SMTL ID : 3py4.1

Crystal structure of bovine lactoperoxidase in complex with paracetamol at 2.4A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.42 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: 6 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217 No protein-ligand interaction detected (PLIP)

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(Covalent)

NAG-NAG-MAN.2: 3 residues within 4Å: Chain A: N.241, A.244, W.384 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 HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 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, Y.312, T.344, F.347, R.348, G.350, H.351, V.354, F.380, L.417, L.421, Q.423, L.433, I.436, R.440 Ligands: TYL.22 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:Q.259, A:F.347, A:F.347, A:F.347, A:R.348, A:V.354, A:V.354, A:F.380, A:L.417, A:L.421, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Water bridges: A:R.255 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

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

NAG.5: 4 residues within 4Å: Chain A: N.95, R.96, I.315 Ligands: IOD.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 NAG.6: 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

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

IOD.7: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: E.77, N.80, P.145 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.95, R.96 Ligands: NAG.5 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 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: R.397, I.559, T.560 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain A: E.88, V.91, P.355, S.356 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: I.387 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: L.224, A.225, R.271 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: S.359, P.367 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: H.377, H.429 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP

1 x TYL: N-(4-HYDROXYPHENYL)ACETAMIDE (TYLENOL)(Non-covalent)

TYL.22: 7 residues within 4Å: Chain A: Q.105, H.109, F.254, R.255, E.258, F.381 Ligands: HEM.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.255, A:E.258, A:F.381 Hydrogen bonds: A:Q.105 Water bridges: A:R.255

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.23: 3 residues within 4Å: Chain A: S.198, L.199, R.202 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.199 Hydrogen bonds: A:R.202

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

SCN.24: 3 residues within 4Å: Chain A: N.230, P.236, C.248 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.25: 3 residues within 4Å: Chain A: W.368, K.388, D.389 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.388 EDO.26: 3 residues within 4Å: Chain A: P.197, A.200, S.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.197

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.27: 4 residues within 4Å: Chain A: L.36, S.334, D.336, R.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, N. et al., Crystal structure of bovine lactoperoxidase in complex with paracetamol at 2.4A resolution. To be published

Release Date

2011-01-05

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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