SMTL ID : 4qjq.1

Crystal structure of goat lactoperoxidase in complex with octopamine at 2.1 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

HEM.1: 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, F.380, L.417, L.421, Q.423, L.433, I.436, R.440 Ligands: OTR.14 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:Q.105, A:Q.259, A:F.347, A:R.348, A:V.354, A:F.380, A:L.417, A:L.421, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:A.114 Water bridges: A:A.114, A:T.344, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.1

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

NAG.2: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.388 NAG.3: 4 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:Q.568 NAG.4: 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 NAG.5: 7 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.205, A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:Q.217, A:Q.217

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 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

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

IOD.7: 5 residues within 4Å: Chain A: R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: W.530 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: P.236 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: A.225, R.278 Ligand excluded by PLIP IOD.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain A: R.397, I.559, T.560, K.561 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: N.95, R.96, R.506 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: S.359, E.373, K.402 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain A: L.199, R.202 Ligand excluded by PLIP

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

SCN.13: 4 residues within 4Å: Chain A: N.230, V.232, P.236, C.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.230

1 x OTR: 4-(2R-AMINO-1-HYDROXYETHYL)PHENOL(Non-covalent)

OTR.14: 8 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258, F.381, Q.423, P.424 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.255, A:R.255, A:E.258, A:F.381 Hydrogen bonds: A:Q.105, A:Q.423

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

PEG.15: 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:N.80, A:K.150, A:R.418 PEG.16: 4 residues within 4Å: Chain A: R.45, W.46, L.47, P.48 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.49

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

EDO.24: 4 residues within 4Å: Chain A: A.35, L.36, R.41, R.338 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.35, A:A.35, A:G.37 EDO.25: 3 residues within 4Å: Chain A: H.377, T.378, H.429 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R.P. et al., Crystal structure of goat lactoperoxidase in complex with octopamine at 2.1 Angstrom resolution. To be Published

Release Date

2014-06-18

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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