SMTL ID : 4pnx.1

Crystal structure of the complex of lactoperoxidase with bromo methane at 2.41 angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 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(Non-covalent)

HEM.2: 24 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, L.376, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: BMM.7 20 PLIP interactions: 20 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:L.376, A:F.380, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Salt bridges: A:R.255, A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

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

NAG.3: 4 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 NAG.4: 6 residues within 4Å: Chain A: N.205, S.208, L.212, A.214, V.215, Q.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.208, A:V.215 Water bridges: A:N.205 NAG.5: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.241, A:A.244, A:K.388 NAG.6: 2 residues within 4Å: Chain A: N.332, S.334 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332

1 x BMM: BROMOMETHANE(Non-covalent)

BMM.7: 5 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: HEM.2 No protein-ligand interaction detected (PLIP)

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

IOD.8: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: N.95, R.96, R.506 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain A: L.12 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: E.77, N.80, P.145 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: S.359, E.373 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: H.377, T.378 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain A: P.375 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: T.23, I.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Structure of bovine lactoperoxidase with a partially linked heme moiety at 1.98 angstrom resolution. Biochim.Biophys.Acta (2017)

Release Date

2014-03-12

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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