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Crystal structure of human ketohexokinase

Analyse Crystal structure of human ketohexokinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HLZ
Type: protein
Length: 1,195 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ketohexokinase
EC: 2.7.1.3
UniProt: P50053
Ligands: UNX
Pockets: 11 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ketohexokinase (EC 2.7.1.3)	protein	296	38% helix, 26% strand	P50053
C	Ketohexokinase (EC 2.7.1.3)	protein	302	37% helix, 26% strand	P50053
D	Ketohexokinase (EC 2.7.1.3)	protein	301	37% helix, 26% strand	P50053

Ligands and binding sites

UNX · Unknown atom or ion · ion · 32 copies · chains A, C, B, D

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	628	0.77	0.83	62	UNX
2	666	0.77	0.82	60	UNX
3	640	0.76	0.82	61	UNX
4	687	0.74	0.80	55	UNX
5	430	0.62	0.76	52	UNX

Interfaces

5 interfaces between chains.

A–D · 1301 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1257 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1016 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 1000 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 62 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

2HLZ · Crystal Structure of human ketohexokinase · the same entry in another collection · chain A against A, TM-score 1.00
P50053 · AlphaFold monomer V2.0 prediction for ketohexokinase (P50053) · a predicted model of the same protein · chain A 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 P50053
Elsewhere: RCSB PDB 2HLZ · PDBe 2HLZ · UniProt P50053

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