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Crystal structure of inhibitor-bound galactokinase

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

PDB: 7S49
Type: protein
Length: 782 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galactokinase
EC: 2.7.1.6
UniProt: P51570
Ligands: 4QI, GLA, NA, PO4
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Galactokinase (EC 2.7.1.6)	protein	391	43% helix, 23% strand	P51570

Ligands and binding sites

4QI · (4R)-2-[(1,3-benzoxazol-2-yl)amino]-4-(4-chloro-1H-pyrazol-5-yl)-4,6,7,8-tetrahydroquinazolin-5(1H)-one · ligand · 2 copies · chains A, B
GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 4 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1098	0.79	0.81	71	empty
2	406	0.77	0.86	53	GLA, 4QI, PO4
3	376	0.75	0.86	56	GLA, 4QI, PO4
4	265	0.59	0.79	40	empty
5	57	0.48	0.85	18	empty

Interfaces

1 interface between chains.

A–B · 856 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7S49 · Crystal Structure of Inhibitor-bound Galactokinase · the same entry in another collection · chain A against A, TM-score 1.00
P51570 · AlphaFold monomer V2.0 prediction for galactokinase (P51570) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P51570
Elsewhere: RCSB PDB 7S49 · PDBe 7S49 · UniProt P51570

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