MolNFT v1 · #113453 · protein

T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-1238

5AFX · Farnesyl pyrophosphate synthase: “T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-1238”. X-ray diffraction, 2 ligands (PVZ, MG), 8 pockets (best druggability 0.83). MolNFT v1 #113453 on GenesisL1: 3D…

PDB: 5AFX
Type: protein
Length: 714 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Farnesyl pyrophosphate synthase
UniProt: Q86C09
Ligands: PVZ, MG
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Farnesyl pyrophosphate synthase	protein	357	74% helix, 1% strand	Q86C09

Ligands and binding sites

PVZ · [1-hydroxy-2-(1-nonyl-1H-3lambda~5~-imidazol-3-yl)ethane-1,1-diyl]bis(phosphonic acid) · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 6 copies · chains A, B

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

Pockets

8 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	450	0.83	0.91	56	MG, PVZ
2	493	0.81	0.88	62	MG, PVZ
3	58	0.48	0.85	19	empty
4	106	0.44	0.78	15	empty
5	122	0.43	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 3175 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

5AFX · T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-1238 · 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 Q86C09
Elsewhere: RCSB PDB 5AFX · PDBe 5AFX · UniProt Q86C09

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.