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Crystal structure of st. JOHN'S wort hyp-1 protein in complex with melatonin

Analyse Crystal structure of st. JOHN'S wort hyp-1 protein in complex with melatonin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I8F
Type: protein
Length: 164 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phenolic oxidative coupling protein
Ligands: ML1, NA, UNL
Pockets: 2 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phenolic oxidative coupling protein	protein	164	29% helix, 41% strand	—

Ligands and binding sites

ML1 · N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide · ligand · 2 copies · chains A
NA · Sodium ion · metal · 3 copies · chains A
UNL · Unknown ligand · ion · 6 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	513	0.81	0.87	50	UNL, NA, ML1
2	51	0.34	0.78	11	ML1

Compared structures

5I8F · Crystal structure of St. John's wort Hyp-1 protein in complex with melatonin · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5I8F · PDBe 5I8F

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