SMTL ID : 5i8f.1

Crystal structure of St. John's wort Hyp-1 protein in complex with melatonin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

6 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.1: 4 residues within 4Å: Ligands: UNL.2, UNL.3, UNL.5, UNL.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.33, A:R.33 UNL.2: 4 residues within 4Å: Chain A: Y.150 Ligands: UNL.1, UNL.5, UNL.6 No protein-ligand interaction detected (PLIP) UNL.3: 2 residues within 4Å: Ligands: UNL.1, UNL.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.29, A:R.33 UNL.4: 2 residues within 4Å: Chain A: L.25 Ligands: UNL.5 No protein-ligand interaction detected (PLIP) UNL.5: 5 residues within 4Å: Chain A: L.29 Ligands: UNL.1, UNL.2, UNL.3, UNL.4 No protein-ligand interaction detected (PLIP) UNL.6: 3 residues within 4Å: Chain A: A.146 Ligands: UNL.1, UNL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.146 Water bridges: A:Y.150

3 x NA: SODIUM ION(Non-functional Binders)

NA.7: 4 residues within 4Å: Chain A: V.66, D.67, H.69, L.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.71 NA.8: 4 residues within 4Å: Chain A: E.16, E.17, Y.150, K.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.16, A:E.17, A:K.151 Water bridges: A:E.17 NA.9: 3 residues within 4Å: Chain A: V.124, G.142, E.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.142

2 x ML1: N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide(Non-covalent)

ML1.10: 14 residues within 4Å: Chain A: R.33, L.37, Q.41, V.44, F.45, H.69, L.71, V.97, Y.107, Y.126, G.142, K.145, A.146, F.149 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.44, A:L.71, A:K.145 Hydrogen bonds: A:H.69 Water bridges: A:R.99, A:F.149 pi-Stacking: A:F.45, A:F.65 ML1.11: 6 residues within 4Å: Chain A: V.36, K.39, A.40, Q.152, V.153, Y.156 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.36, A:K.39, A:Y.156, A:Y.156 Hydrogen bonds: A:Q.152 pi-Stacking: A:Y.156, A:Y.156

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 4 residues within 4Å: Chain A: E.17, S.18, P.19 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.17, A:S.18 Water bridges: A:S.118 GOL.13: 3 residues within 4Å: Chain A: P.19, E.154 Ligands: GOL.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sliwiak, J. et al., Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin. Front Plant Sci (2016)

Release Date

2016-05-25

Peptides

Phenolic oxidative coupling protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phenolic oxidative coupling protein

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