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Glycerol kinase H232E with ethylene glycol

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

PDB: 3H45
Type: protein
Length: 1,998 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycerol kinase
EC: 2.7.1.30
UniProt: O34153
Ligands: PO4
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Glycerol kinase (EC 2.7.1.30)	protein	499	37% helix, 23% strand	O34153
O	Glycerol kinase (EC 2.7.1.30)	protein	500	37% helix, 23% strand	O34153
C	Glycerol kinase (EC 2.7.1.30)	protein	500	38% helix, 24% strand	O34153
D	Glycerol kinase (EC 2.7.1.30)	protein	499	36% helix, 23% strand	O34153

Ligands and binding sites

PO4 · Phosphate ion · ion · 6 copies · chains X, O, C, D
EDO · 1,2-ethanediol · additive · 5 copies · chains X, O, C, D

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	598	0.75	0.82	70	EDO, PO4
2	744	0.75	0.80	70	EDO, PO4
3	551	0.73	0.81	52	EDO, PO4
4	1180	0.72	0.76	89	empty
5	530	0.72	0.81	48	EDO, PO4

Interfaces

3 interfaces between chains.

C–D · 618 Å² buried · 3 hydrogen bonds · protein-protein
X–O · 511 Å² buried · 1 hydrogen bond · protein-protein
X–D · 146 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3H45 · Glycerol Kinase H232E with Ethylene Glycol · the same entry in another collection · chain D against D, TM-score 1.00
O34153 · AlphaFold monomer V2.0 prediction for glycerol kinase (O34153) · a predicted model of the same protein · chain O 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 3H45 · PDBe 3H45 · UniProt O34153

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