SMTL ID : 3r5o.1

Crystal structure of the complex of bovine lactoperoxidase with 4-allyl-2-methoxyphenol at 2.6 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 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 CA: CALCIUM ION(Non-covalent)

CA.2: 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:F.186, A:S.190

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 24 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, Q.423, L.433, I.436, R.440 Ligands: EUG.17 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Q.105, A:E.258, 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.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 Metal complexes: A:H.351, H2O.6

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

NAG.4: 5 residues within 4Å: Chain A: N.95, R.96, I.315 Ligands: IOD.9, GOL.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 NAG.5: 7 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 NAG.6: 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

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

IOD.7: 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.8: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.95, R.96 Ligands: NAG.4 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: W.530 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: R.397, I.559, T.560 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: S.359, P.367, E.373 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: N.216, F.229 Ligand excluded by PLIP

1 x EUG: 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol(Non-covalent)

EUG.17: 8 residues within 4Å: Chain A: H.109, F.113, F.254, R.255, E.258, F.381 Ligands: HEM.3, SCN.19 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.254, A:R.255, A:R.255, A:E.258, A:F.381, A:F.381 Water bridges: A:Q.105

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.18: 3 residues within 4Å: Chain A: S.198, L.199, R.202 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.199 Hydrogen bonds: A:R.202

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

SCN.19: 4 residues within 4Å: Chain A: S.235, C.248, F.254 Ligands: EUG.17 No protein-ligand interaction detected (PLIP)

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

EDO.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.21: 2 residues within 4Å: Chain A: E.123, H.124 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.123, A:S.125, A:S.125

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 3 residues within 4Å: Chain A: Q.94, N.95 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, N. et al., Crystal structure of the complex of bovine lactoperoxidase with 4-allyl-2-methoxyphenol at 2.6 A resolution. To be Published

Release Date

2011-08-17

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

Related Entries With Identical Sequence