Research workbench

Structure of SYM2 D9V+D55V+D130V+D176V

Analyse Structure of SYM2 D9V+D55V+D130V+D176V in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FX7
Type: protein
Length: 960 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Imidazole glycerol phosphate synthase subunit hisf
EC: 4.1.3.-
UniProt: Q9X0C6
Ligands: PI
Pockets: 8 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Imidazole glycerol phosphate synthase subunit hisf (EC 4.1.3.-)	protein	240	39% helix, 30% strand	Q9X0C6
B	Imidazole glycerol phosphate synthase subunit hisf (EC 4.1.3.-)	protein	241	39% helix, 30% strand	Q9X0C6
C	Imidazole glycerol phosphate synthase subunit hisf (EC 4.1.3.-)	protein	240	37% helix, 30% strand	Q9X0C6
D	Imidazole glycerol phosphate synthase subunit hisf (EC 4.1.3.-)	protein	239	41% helix, 30% strand	Q9X0C6

Ligands and binding sites

PI · Hydrogenphosphate ion · ion · 8 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	976	0.85	0.86	100	PI
2	501	0.79	0.86	64	PI
3	279	0.79	0.91	42	PI
4	314	0.79	0.90	45	PI
5	279	0.60	0.79	28	empty

Interfaces

5 interfaces between chains.

A–B · 455 Å² buried · 1 hydrogen bond · protein-protein
B–C · 409 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 396 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 171 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 62 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4FX7 · Structure of Sym2 D9V+D55V+D130V+D176V · the same entry in another collection · chain D against D, TM-score 1.00
Q9X0C6 · AlphaFold monomer V2.0 prediction for imidazole glycerol phosphate synthase subunit hisf… · a predicted model of the same protein · chain B against A, TM-score 0.91

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 Q9X0C6
Elsewhere: RCSB PDB 4FX7 · PDBe 4FX7 · UniProt Q9X0C6

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