6Q90 | pdb_00006q90

Structure of human galactokinase 1 bound with 1-(4-Methoxyphenyl)-3-(4-pyridinyl)urea

• PDB DOI: https://doi.org/10.2210/pdb6Q90/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-12-16 Released: 2019-01-23 
• Deposition Author(s): Mackinnon, S.R., Bezerra, G.A., Zhang, M., Foster, W., Krojer, T., Brandao-Neto, J., Douangamath, A., Arrowsmith, C., Edwards, A., Bountra, C., Brennan, P., Lai, K., Yue, W.W.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structure of human galactokinase 1 bound with 1-(4-Methoxyphenyl)-3-(4-pyridinyl)urea

Mackinnon, S.R., Bezerra, G.A., Zhang, M., Foster, W., Krojer, T., Brandao-Neto, J., Douangamath, A., Arrowsmith, C., Edwards, A., Bountra, C., Brennan, P., Lai, K., Yue, W.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 170.92 kDa 
• Atom Count: 11,344 
• Modelled Residue Count: 1,546 
• Deposited Residue Count: 1,568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactokinase	A, B, C, D	392	Homo sapiens	Mutation(s): 2  Gene Names: GALK1, GALK EC: 2.7.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P51570 (Homo sapiens) Explore P51570  Go to UniProtKB:  P51570
PHAROS:  P51570 GTEx:  ENSG00000108479

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HFK	F [auth A], H [auth B], J [auth C]	2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one C20 H22 N4 O2 AZBGHUMVHJKFOO-UHFFFAOYSA-N
JHJ	K [auth C], L [auth D]	N-(4-methoxyphenyl)-N'-pyridin-4-ylurea C13 H13 N3 O2 IFKGCTGEAFOLOL-UHFFFAOYSA-N
GAL	E [auth A], G [auth B], I [auth C]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.55	α = 90
b = 114.51	β = 100.33
c = 120.81	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Mackinnon, S.R., Bezerra, G.A., Zhang, M., Foster, W., Krojer, T., Brandao-Neto, J., Douangamath, A., Arrowsmith, C., Edwards, A., Bountra, C., Brennan, P., Lai, K., Yue, W.W.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	092809/Z/10/Z

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-20
  Changes: Structure summary