SMTL ID : 4njb.1

Crystal structure of the complex of lactoperoxidase from bovine with 3,3-oxydipyridine at 2.31 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

monomer

Ligands

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.1: 7 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217, A:Q.217 NAG-NAG.2: 3 residues within 4Å: Chain A: N.241, A.244, W.384 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4: 25 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, L.421, Q.423, L.433, I.436, R.440 Ligands: 3OP.21 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Q.105, A:Q.105, A:Q.259, A:F.347, A:F.347, A:R.348, A:V.354, A:V.354, A:L.376, A:F.380, A:L.417, A:L.421, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Water bridges: A:R.348, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.17

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

NAG.5: 4 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 Water bridges: A:R.96, A:Q.568 NAG.6: 3 residues within 4Å: Chain A: N.332, S.334, V.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:D.336

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

IOD.7: 4 residues within 4Å: Chain A: R.397, I.559, T.560, K.561 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.236, T.425 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: A.225, R.271, R.278 Ligand excluded by PLIP IOD.14: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: W.530 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain A: R.202 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: S.359, L.361, P.367 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 6 residues within 4Å: Chain A: R.76, N.80, P.149, K.150, R.418, N.419 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.76, A:R.418, A:N.419 Water bridges: A:N.80

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.19: 4 residues within 4Å: Chain A: F.229, V.246, I.387, K.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.388 EDO.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x 3OP: 3,3'-oxydipyridine(Non-covalent)

3OP.21: 7 residues within 4Å: Chain A: Q.105, H.109, F.254, R.255, E.258, F.381 Ligands: HEM.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.254, A:E.258 Water bridges: A:Q.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamini, S. et al., Crystal structure of the complex of lactoperoxidase from bovine with 3,3-oxydipyridine at 2.31 A resolution. To be Published

Release Date

2013-11-27

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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