SMTL ID : 3qf1.1

Crystal structure of the complex of caprine lactoperoxidase with diethylenediamine at 2.6A resolution

Coordinates

PDB Format Compare

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)

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

NAG.2: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:N.205, A:N.205 NAG.3: 2 residues within 4Å: Chain A: N.332, S.334 No protein-ligand interaction detected (PLIP)

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:T.184, A:T.184, A:F.186, A:S.190

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 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: PZE.16 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:E.258, 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:A.114 Water bridges: A:R.348, A:R.348 Salt bridges: A:R.348, A:R.440 Metal complexes: A:H.351, H2O.5

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

IOD.6: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: N.216, F.229 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: N.80, P.145 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: 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: 2 residues within 4Å: Chain A: H.377, H.429 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: L.199, R.202 Ligand excluded by PLIP

1 x PZE: piperazine(Non-covalent)

PZE.16: 4 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.109 Water bridges: A:Q.105

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

SCN.17: 2 residues within 4Å: Chain A: N.230, V.232 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 6 residues within 4Å: Chain A: S.359, L.361, P.367, A.372, E.373, K.402 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.402 Water bridges: A:Q.366

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

EDO.19: 1 residues within 4Å: Chain A: S.580 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.580

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, N. et al., Crystal structure of the complex of caprine lactoperoxidase with diethylenediamine at 2.6A resolution. To be Published

Release Date

2011-04-27

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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