SMTL ID : 2nqx.1

Crystal Structure of bovine lactoperoxidase with iodide ions at 2.9A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 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

NAG-NAG-MAN.1: 6 residues within 4Å: Chain A: N.95, I.315, R.504, H.565, Q.568 Ligands: CO3.13 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

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.2: 8 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217, W.220 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.217 NAG-NAG.4: 2 residues within 4Å: Chain A: N.332, V.335 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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

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

IOD.6: 5 residues within 4Å: Chain A: R.45, W.46, L.47, V.342, W.452 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: E.77, N.80, P.145 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: P.197, S.198 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: N.216, E.218, 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: K.462, T.463 Ligand excluded by PLIP

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.13: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG-NAG-MAN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.504, A:R.506

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.14: 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, F.380, L.417, L.421, Q.423, L.433, I.436, R.440 Ligands: OSM.15 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, 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:I.436 Hydrogen bonds: A:D.112, A:A.114 Water bridges: A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

1 x OSM: 1-(OXIDOSULFANYL)METHANAMINE(Non-covalent)

OSM.15: 5 residues within 4Å: Chain A: H.109, R.255, E.258, F.381 Ligands: HEM.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Crystal Structure of bovine lactoperoxidase with iodide ions at 2.9A resolution. To be Published

Release Date

2006-11-21

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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