SMTL ID : 2pt3.1

Crystal structure of bovine lactoperoxidase at 2.34 A resolution reveals multiple anion binding sites

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 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: 7 residues within 4Å: Chain A: N.95, R.96, I.315, R.504, H.565, Q.568 Ligands: PO4.9 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: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217, A:Q.217 NAG-NAG.4: 3 residues within 4Å: Chain A: N.332, S.334, 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

16 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 5 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: HEM.22 Ligand excluded by PLIP PO4.7: 9 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, S.340, N.341, V.342, M.446, W.452 Ligand excluded by PLIP PO4.8: 5 residues within 4Å: Chain A: E.77, N.80, K.81, P.145, N.147 Ligand excluded by PLIP PO4.9: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG-NAG-MAN.1 Ligand excluded by PLIP PO4.10: 3 residues within 4Å: Chain A: S.198, L.199, R.202 Ligand excluded by PLIP PO4.11: 5 residues within 4Å: Chain A: N.216, Q.217, E.218, P.228, F.229 Ligand excluded by PLIP PO4.12: 6 residues within 4Å: Chain A: G.223, L.224, A.225, R.271, N.274, R.278 Ligand excluded by PLIP PO4.13: 7 residues within 4Å: Chain A: P.234, S.235, P.236, F.239, F.422, P.424, T.425 Ligand excluded by PLIP PO4.14: 6 residues within 4Å: Chain A: I.306, F.309, R.310, W.529, W.530, E.531 Ligand excluded by PLIP PO4.15: 7 residues within 4Å: Chain A: S.359, R.360, L.361, P.367, A.372, E.373, K.402 Ligand excluded by PLIP PO4.16: 3 residues within 4Å: Chain A: H.377, T.378, H.429 Ligand excluded by PLIP PO4.17: 7 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, I.559, T.560, K.561 Ligand excluded by PLIP PO4.18: 4 residues within 4Å: Chain A: P.461, K.462, T.463, G.466 Ligand excluded by PLIP PO4.19: 4 residues within 4Å: Chain A: R.551, C.579, S.580, K.584 Ligand excluded by PLIP PO4.20: 4 residues within 4Å: Chain A: D.311, H.565, A.566, F.567 Ligand excluded by PLIP PO4.21: 1 residues within 4Å: Chain A: R.593 Ligand excluded by PLIP

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.22: 23 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, Q.423, L.433, I.436, R.440 Ligands: PO4.6 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:E.258, A:Q.259, A:F.347, A:F.347, A:R.348, A:V.354, A:V.354, A:F.380, A:L.417, A:L.433, A:L.433 Hydrogen bonds: A:D.112, A:A.114 Water bridges: A:A.114 Salt bridges: A:R.255, A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Crystal structure of bovine lactoperoxidase at 2.34 A resolution reveals multiple anion binding sites. To be Published

Release Date

2007-05-22

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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