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Crystal structure of the C-terminal hexokinase domain of human HK3

Analyse Crystal structure of the C-terminal hexokinase domain of human HK3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HM8
Type: protein
Length: 1,755 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hexokinase-3
EC: 2.7.1.1
UniProt: P52790
Ligands: GLC, BG6
Pockets: 19 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hexokinase-3 (EC 2.7.1.1)	protein	441	46% helix, 17% strand	P52790
C	Hexokinase-3 (EC 2.7.1.1)	protein	436	46% helix, 18% strand	P52790
D	Hexokinase-3 (EC 2.7.1.1)	protein	437	46% helix, 19% strand	P52790

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

19 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	1049	0.77	0.79	121	empty
2	865	0.76	0.79	107	empty
3	227	0.68	0.85	36	GLC, BG6
4	51	0.66	0.95	16	empty
5	223	0.65	0.84	36	GLC, BG6

Interfaces

4 interfaces between chains.

A–C · 961 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 659 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 353 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 43 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3HM8 · Crystal structure of the C-terminal Hexokinase domain of human HK3 · the same entry in another collection · chain A against A, TM-score 1.00
P52790 · AlphaFold monomer V2.0 prediction for hexokinase-3 (P52790) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P52790
Elsewhere: RCSB PDB 3HM8 · PDBe 3HM8 · UniProt P52790

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