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Crystal structure of lavandulyl diphosphate synthase from lavandula X intermedia in complex with S-thiolo-isopentenyldiphosphate

Analyse Crystal structure of lavandulyl diphosphate synthase from lavandula X… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HC7
Type: protein
Length: 230 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prenyltransference for protein
Ligands: DST, MG
Pockets: 1 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prenyltransference for protein	protein	230	52% helix, 14% strand	—

Ligands and binding sites

DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	134	0.60	0.85	22	MG, DST

Compared structures

5HC7 · Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5HC7 · PDBe 5HC7

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