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PagF prenyltransferase with Tyr-Tyr-Tyr and DMSPP

Analyse PagF prenyltransferase with Tyr-Tyr-Tyr and DMSPP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TU5
Type: protein
Length: 300 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.9
Source: Planktothrix agardhii NIES-596; SYNTHETIC CONSTRUCT
Molecule: PagF prenyltransferase; Tyr-tyr-tyr
UniProt: F5B6Z0
Ligands: DST, MG
Pockets: 2 · best druggability 0.66

Structure

x-ray diffraction · resolution 1.9 · 2 distinct chains · 42% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PagF prenyltransferase	protein	297	42% helix, 29% strand	F5B6Z0
B	Tyr-tyr-tyr	protein	3	0% helix, 0% strand	—

Ligands and binding sites

DST · Dimethylallyl S-thiolodiphosphate · ligand · chains A, B
MG · Magnesium ion · metal · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	249	0.66	0.83	37	DST, MG
2	139	0.50	0.79	26	empty

Interfaces

1 interface between chains.

A–B · 404 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5TU5 · Pagf prenyltransferase with tyr-tyr-tyr and dmspp · 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 F5B6Z0
Elsewhere: RCSB PDB 5TU5 · PDBe 5TU5 · UniProt F5B6Z0

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