SMTL ID : 3uba.1

Crystal structure of the complex of bovine lactoperoxidase with p-hydroxycinnamic acid at 2.6 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 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: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 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: HC4.17 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: 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:F.380, A:L.417, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Salt bridges: A:R.348, A:R.348, A:R.440 pi-Stacking: A:H.351 Metal complexes: A:H.351

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

NAG.3: 5 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: GOL.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 NAG.4: 6 residues within 4Å: Chain A: N.205, S.208, L.212, A.214, V.215, Q.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.205, A:S.208, A:V.215, A:Q.217, A:Q.217 NAG.5: 3 residues within 4Å: Chain A: N.332, S.334, V.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332

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

IOD.6: 3 residues within 4Å: Chain A: R.397, I.559, T.560 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: N.216, F.229 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.12: 7 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, M.446, W.452 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: R.202 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.15: 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:T.184, A:T.184, A:D.188, A:S.190

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.16: 5 residues within 4Å: Chain A: N.230, P.236, C.248, F.254 Ligands: HC4.17 No protein-ligand interaction detected (PLIP)

1 x HC4: 4'-HYDROXYCINNAMIC ACID(Non-covalent)

HC4.17: 9 residues within 4Å: Chain A: Q.105, H.109, F.254, R.255, E.258, F.381, P.424 Ligands: HEM.2, SCN.16 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.255, A:R.255, A:E.258, A:F.381 Hydrogen bonds: A:Q.105

2 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:K.150, A:R.418, A:N.419 PEG.19: 6 residues within 4Å: Chain A: N.30, R.32, S.33, L.36, N.333, D.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:D.336 Water bridges: A:S.33

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.506, A:R.506

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

EDO.21: 2 residues within 4Å: Chain A: R.245, V.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.245 EDO.22: 1 residues within 4Å: Chain A: K.472 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, N. et al., Crystal structure of the complex of bovine lactoperoxidase with p-hydroxycinnamic acid at 2.6 A resolution. to be published

Release Date

2011-12-28

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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