MolNFT v1 · #113516 · protein

T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-1326

5AHU · Farnesyl pyrophosphate synthase, putative: “T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-1326”. X-ray diffraction, 2 ligands (G76, MG), 6 pockets (best druggability 0.82). MolNFT v1 #113516 on GenesisL1…

PDB: 5AHU
Type: protein
Length: 714 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Farnesyl pyrophosphate synthase, putative; Farnesyl pyrophosphate synthase
EC: 2.5.1.10
UniProt: C9ZSP7, Q86C09
Ligands: G76, MG
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Farnesyl pyrophosphate synthase, putative (EC 2.5.1.10)	protein	63	83% helix, 0% strand	C9ZSP7
B, D	Farnesyl pyrophosphate synthase	protein	294	73% helix, 1% strand	Q86C09

Ligands and binding sites

G76 · [2-(1-heptyl-1H-imidazol-3-ium-3-yl)ethane-1,1-diyl]bis(phosphonate) · ligand · 2 copies · chains B, D
MG · Magnesium ion · metal · 6 copies · chains B, D

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

Pockets

6 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	415	0.82	0.91	62	G76, MG
2	443	0.82	0.89	61	G76, MG
3	111	0.43	0.77	13	empty
4	110	0.42	0.76	13	empty
5	62	0.34	0.77	10	empty

Interfaces

5 interfaces between chains.

A–B · 1997 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1996 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 1876 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 800 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 787 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5AHU · T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-1326 · 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 C9ZSP7
Every structure of UniProt Q86C09
Elsewhere: RCSB PDB 5AHU · PDBe 5AHU · UniProt C9ZSP7 · UniProt Q86C09

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