Research workbench

IspG in complex with Inhibitor 7 (compound 1061)

Analyse IspG in complex with Inhibitor 7 (compound 1061) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4S3E
Type: protein
Length: 401 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.35
Source: Thermus thermophilus HB8
Molecule: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
EC: 1.17.7.1
UniProt: Q5SLI8
Ligands: SF4, 0CG
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · resolution 1.35 · 1 distinct chain · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.7.1)	protein	401	47% helix, 17% strand	Q5SLI8

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains A
0CG · prop-2-yn-1-yl trihydrogen diphosphate · ligand · chains A
GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	143	0.43	0.75	24	GOL
2	110	0.41	0.76	17	empty
3	109	0.37	0.75	20	empty

Modifications

Observed in the structure: 1 modified (carboxylation).

Compared structures

4S3E · Ispg in complex with inhibitor 7 (compound 1061) · the same entry in another collection · chain A against A, TM-score 1.00
Q5SLI8 · AlphaFold monomer V2.0 prediction for 4-hydroxy-3-methylbut-2-en-1-yl diphosphate… · a predicted model of the same protein · 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 Q5SLI8
Elsewhere: RCSB PDB 4S3E · PDBe 4S3E · UniProt Q5SLI8

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