MolNFT v1 · #65668 · protein

Glycerol kinase H232R with ethylene glycol

3H3O: “Glycerol kinase H232R with ethylene glycol”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.75). MolNFT v1 #65668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3H3O
Type: protein
Length: 1,994 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 · 3 distinct chains · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O	Glycerol kinase (EC 2.7.1.30)	protein	498	38% helix, 24% strand	O34153
X, B	Glycerol kinase (EC 2.7.1.30)	protein	499	37% helix, 24% strand	O34153
C	Glycerol kinase (EC 2.7.1.30)	protein	498	36% helix, 23% strand	O34153

Ligands and binding sites

PO4 · Phosphate ion · ion · 7 copies · chains O, X, B, C
EDO · 1,2-ethanediol · additive · 10 copies · chains O, X, B, C

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	714	0.75	0.80	74	EDO, PO4
2	606	0.74	0.81	76	EDO, PO4
3	499	0.73	0.82	47	EDO, PO4
4	507	0.73	0.82	51	EDO, PO4
5	1162	0.73	0.76	93	empty

Interfaces

3 interfaces between chains.

O–X · 476 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 455 Å² buried · 0 hydrogen bonds · protein-protein
O–C · 181 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3H3O · Glycerol Kinase H232R with Ethylene Glycol · the same entry in another collection · chain O against O, 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 3H3O · PDBe 3H3O · UniProt O34153

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