SMTL ID : 2o86.1

Crystal structure of a ternary complex of buffalo lactoperoxidase with nitrate and iodide at 2.8 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 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, R.96, I.315, R.504, H.565 Ligands: CO3.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.504 Water bridges: A:R.504 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: 6 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217, W.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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:T.184, A:F.186

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

CO3.6: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG-NAG-MAN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.504, A:R.504, A:R.506, A:R.506

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

IOD.7: 4 residues within 4Å: Chain A: N.216, Q.217, E.218, F.229 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.21 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: P.236, P.424 Ligand excluded by PLIP IOD.10: 5 residues within 4Å: Chain A: E.363, R.397, I.559, T.560, K.561 Ligand excluded by PLIP IOD.11: 5 residues within 4Å: Chain A: W.46, N.341, V.342, M.446, W.452 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: K.462, T.463 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: S.359, P.367, K.402 Ligand excluded by PLIP

7 x NO3: NITRATE ION(Non-functional Binders)

NO3.14: 4 residues within 4Å: Chain A: Y.85, L.86, D.87, K.411 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.86, A:D.87, A:K.411 NO3.15: 4 residues within 4Å: Chain A: R.31, Y.331, N.333, R.527 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.31 Water bridges: A:N.333 NO3.16: 2 residues within 4Å: Chain A: S.198, L.199 No protein-ligand interaction detected (PLIP) NO3.17: 7 residues within 4Å: Chain A: E.77, N.80, K.81, P.145, K.146, N.147, D.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.80, A:N.147 NO3.18: 3 residues within 4Å: Chain A: E.196, P.197, S.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.198, A:S.198 NO3.19: 6 residues within 4Å: Chain A: I.306, F.309, R.310, W.529, W.530, E.531 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.306, A:R.310 NO3.20: 3 residues within 4Å: Chain A: H.377, T.378, H.429 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.377

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.21: 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, L.376, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: IOD.8 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:E.258, A:F.347, A:F.347, A:V.354, A:V.354, A:L.376, A:F.380, A:L.417, A:L.433, 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.348, A:R.440 Metal complexes: A:H.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sheikh, I.A. et al., Crystal structure of a ternary complex of buffalo lactoperoxidase with nitrate and iodide at 2.8 A resolution. To be Published

Release Date

2006-12-26

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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