Research workbench

Glycerol kinase H232E with glycerol

Analyse Glycerol kinase H232E with glycerol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3H46
Type: protein
Length: 1,000 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycerol kinase
EC: 2.7.1.30
UniProt: O34153
Ligands: SO4
Pockets: 11 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X, O	Glycerol kinase (EC 2.7.1.30)	protein	500	37% helix, 24% strand	O34153

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains X, O
GOL · Glycerol · additive · 2 copies · chains X, O
EDO · 1,2-ethanediol · additive · 2 copies · chains X, O

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

Pockets

11 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	496	0.72	0.82	52	SO4, GOL
2	429	0.72	0.82	51	SO4, GOL
3	109	0.58	0.85	20	empty
4	141	0.57	0.83	23	empty
5	210	0.57	0.79	28	empty

Interfaces

1 interface between chains.

X–O · 550 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3H46 · Glycerol Kinase H232E with Glycerol · the same entry in another collection · chain X against X, TM-score 1.00
O34153 · AlphaFold monomer V2.0 prediction for glycerol kinase (O34153) · a predicted model of the same protein · chain X against A, TM-score 0.99

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 O34153
Elsewhere: RCSB PDB 3H46 · PDBe 3H46 · UniProt O34153

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