MolNFT v1 · #122748 · protein

Crystal structure of a dehydrosqualene synthase in complex with ligand

5IYS · Phytoene synthase: “Crystal structure of a dehydrosqualene synthase in complex with ligand”. X-ray diffraction, 3 ligands (FPS, MG, SO4), 2 pockets (best druggability 0.80). MolNFT v1 #122748 on GenesisL1: 3D structure, binding…

PDB: 5IYS
Type: protein
Length: 283 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phytoene synthase
UniProt: I6T9U8
Ligands: FPS, MG, SO4
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phytoene synthase	protein	283	76% helix, 1% strand	I6T9U8

Ligands and binding sites

FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · 2 copies · chains A
MG · Magnesium ion · metal · 3 copies · chains A
SO4 · Sulfate ion · ion · 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	607	0.80	0.85	53	MG, FPS
2	57	0.42	0.81	16	empty

Compared structures

5IYS · Crystal structure of a dehydrosqualene synthase in complex with ligand · 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
Every structure of UniProt I6T9U8
Elsewhere: RCSB PDB 5IYS · PDBe 5IYS · UniProt I6T9U8

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