SMTL ID : 3nyh.1

Crystal structure of lactoperoxidase complexed simultaneously with thiocyanate ion, iodide ion, bromide ion, chloride ion through the substrate diffusion channel reveals a preferential queue of the inorganic substrates towards the distal heme cavity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 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: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 No protein-ligand interaction detected (PLIP)

1 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(Non-covalent)

NAG-NAG-MAN.2: 5 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 Ligands: GOL.25 No protein-ligand interaction detected (PLIP)

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, Y.312, 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: BR.22 28 PLIP interactions: 27 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:F.347, A:R.348, A:V.354, 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 Water bridges: A:E.116, A:R.348, A:R.348, A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.7

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 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

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 Ligands: IOD.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 Water bridges: A:N.95, A:R.96, A:P.314 NAG.6: 3 residues within 4Å: Chain A: N.332, S.334, V.335 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.332, A:D.336

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

IOD.7: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: N.95, R.96, R.506 Ligands: NAG.5 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: Q.217, F.229 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain A: E.88, V.91, P.355, S.356 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: F.229 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: L.199, R.202 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: A.225, R.271 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: S.359, P.367 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: R.31, Y.331, N.333 Ligand excluded by PLIP

1 x BR: BROMIDE ION(Non-covalent)

BR.22: 4 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.3 Ligand excluded by PLIP

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.23: 2 residues within 4Å: Chain A: F.254, F.381 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 6 residues within 4Å: Chain A: P.234, S.235, E.238, F.239, T.242, R.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.235, A:S.235, A:E.238, A:R.245 GOL.25: 6 residues within 4Å: Chain A: F.239, I.240, N.241, T.242, T.243 Ligands: NAG-NAG-MAN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.239, A:T.242, A:T.243, A:T.243 Water bridges: A:T.242 GOL.26: 3 residues within 4Å: Chain A: H.377, T.378, H.429 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.429 Water bridges: A:H.429

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

PEG.27: 5 residues within 4Å: Chain A: R.76, N.80, P.149, 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

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

MPD.28: 5 residues within 4Å: Chain A: I.24, P.197, A.200, S.201, R.204 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.24, A:P.197 Hydrogen bonds: A:R.204 Water bridges: A:I.24, A:I.24

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

EDO.29: 2 residues within 4Å: Chain A: D.362, E.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.363, A:E.363, A:E.363

1 x ZN: ZINC ION(Non-covalent)

ZN.30: 2 residues within 4Å: Chain A: H.222, H.558 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.222, A:H.558, H2O.15

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

SCN.31: 3 residues within 4Å: Chain A: N.230, P.236, C.248 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.254, A:F.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, N. et al., Crystal structure of lactoperoxidase complexed simultaneously with thiocyanate ion, iodide ion, bromide ion, chloride ion through the substrate diffusion channel reveals a preferential queue of the inorganic substrates towards the distal heme cavity. To be Published

Release Date

2010-10-20

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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