SMTL ID : 2z5z.1

Crystal structure of the complex of buffalo Lactoperoxidase with fluoride ion at 3.5A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 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: 5 residues within 4Å: Chain A: N.95, I.315, R.504, H.565, Q.568 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, M.213, A.214, V.215, Q.217 No protein-ligand interaction detected (PLIP) 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:T.184, A:S.190

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

IOD.6: 4 residues within 4Å: Chain A: N.341, V.342, M.446, W.452 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: R.506 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: R.202 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: N.216, Q.217, E.218, F.229 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: P.424, T.425 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: F.309, R.310 Ligand excluded by PLIP IOD.13: 5 residues within 4Å: Chain A: E.363, Y.365, R.397, I.559, K.561 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain A: P.461, K.462, T.463, G.466 Ligand excluded by PLIP

3 x F: FLUORIDE ION(Non-covalent)

F.15: 3 residues within 4Å: Chain A: S.359, P.367, K.402 No protein-ligand interaction detected (PLIP) F.16: 1 residues within 4Å: Chain A: H.377 No protein-ligand interaction detected (PLIP) F.17: 1 residues within 4Å: Chain A: S.580 No protein-ligand interaction detected (PLIP)

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

HEM.18: 23 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, R.255, E.258, 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.19 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:Q.105, A:F.347, A:R.348, 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 Salt bridges: A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351

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

OSM.19: 4 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sheikh, I.A. et al., Crystal structure of the complex of buffalo Lactoperoxidase with fluoride ion at 3.5A resolution. To be Published

Release Date

2007-08-14

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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