SMTL ID : 3s4f.1

Crystal structure of the complex of bovine lactoperoxidase with 1H-pyrazolo[4,3-c] pyridine at 1.99 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.388 Water bridges: A:K.388 NAG-NAG.2: 6 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 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, Y.312, 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: PZR.15 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:Q.259, A:F.347, 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:A.114 Water bridges: A:R.255, A:R.348, A:R.348 Salt bridges: A:R.348, A:R.440 pi-Cation interactions: A:H.351 Metal complexes: A:H.351, H2O.1

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

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

IOD.5: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: P.236, P.424 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: Q.217, F.229 Ligand excluded by PLIP IOD.8: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: R.397, I.559, T.560, K.561 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: H.377, T.378, H.429 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: N.95, R.96, R.506 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: K.462, T.463 Ligands: PEG.24 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: L.224, A.225 Ligand excluded by PLIP

1 x PZR: 1H-pyrazolo[4,3-c]pyridine(Non-covalent)

PZR.15: 6 residues within 4Å: Chain A: H.109, R.255, E.258, F.381, P.424 Ligands: HEM.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.255, A:E.258 Hydrogen bonds: A:Q.105 Water bridges: A:Q.423

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

NAG.16: 3 residues within 4Å: Chain A: N.332, S.334, V.335 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.332, A:N.332 Water bridges: A:S.334, A:D.336 NAG.17: 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:Q.568, A:Q.568

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

SCN.18: 5 residues within 4Å: Chain A: N.230, K.232, S.235, C.248, F.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.230

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

PEG.19: 6 residues within 4Å: Chain A: R.76, N.80, P.149, K.150, R.418, N.419 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.76, A:N.80, A:K.150, A:K.150, A:R.418, A:R.418, A:N.419 PEG.20: 5 residues within 4Å: Chain A: R.32, L.36, N.333, D.336, R.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.30, A:R.32, A:N.333 PEG.21: 6 residues within 4Å: Chain A: E.218, A.219, F.229, R.245, I.387, K.388 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.245, A:K.388 PEG.22: 5 residues within 4Å: Chain A: V.215, N.216, Q.217, A.219, W.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.218 PEG.23: 5 residues within 4Å: Chain A: P.197, A.200, S.201, R.204, L.206 3 PLIP interactions: 3 interactions with chain A Water bridges: A:I.24, A:I.24, A:R.204 PEG.24: 6 residues within 4Å: Chain A: S.459, Q.460, P.461, T.469, V.470 Ligands: IOD.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.459, A:Q.460 Water bridges: A:Q.460 PEG.25: 3 residues within 4Å: Chain A: K.472, P.500, M.501 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.472

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.26: 3 residues within 4Å: Chain A: S.198, L.199, R.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A. et al., Crystal structure of the complex of bovine lactoperoxidase with 1H-pyrazolo[4,3-c] pyridine at 1.99 A resolution. To be Published

Release Date

2011-06-08

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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