SMTL ID : 4gn6.1

Structure of paracetamol bound bovine lactoperoxidase at 2.45A 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: 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.2: 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:T.184, A:S.190

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 19 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, E.258, Q.259, T.344, F.347, R.348, G.350, H.351, Q.423, L.433, I.436, R.440 Ligands: TYL.20 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Q.105, A:Q.105, A:E.258, A:Q.259, A:F.347, A:F.347, A:R.348, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Salt bridges: A:R.348, A:R.440 Metal complexes: A:H.351, H2O.4

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

NAG.4: 4 residues within 4Å: Chain A: N.95, R.96, I.315 Ligands: IOD.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:N.95 NAG.5: 6 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.205, A:S.208, A:V.215, A:Q.217, A:Q.217 NAG.6: 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 Water bridges: A:Q.520

13 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: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.95, R.96 Ligands: NAG.4 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: 2 residues within 4Å: Chain A: R.397, 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: 2 residues within 4Å: Chain A: F.229, I.387 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: P.461, K.462, T.463, G.466 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: H.377, H.429 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: L.224, A.225, R.271, R.278 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: P.149, N.419 Ligand excluded by PLIP

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

TYL.20: 6 residues within 4Å: Chain A: H.109, F.254, R.255, E.258, F.381 Ligands: HEM.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.254, A:R.255, A:E.258, A:F.381 Hydrogen bonds: A:H.109 Water bridges: A:Q.105

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

MPD.21: 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.22: 3 residues within 4Å: Chain A: N.230, P.236, C.248 No protein-ligand interaction detected (PLIP)

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

EDO.23: 3 residues within 4Å: Chain A: P.197, A.200, S.201 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 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., Structure of paracetamol bound bovine lactoperoxidase at 2.45A resolution. To be Published

Release Date

2012-09-19

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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