6ZGX
Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N-(pyrimidin-2-yl)acetamide
- PDB DOI: https://doi.org/10.2210/pdb6ZGX/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2020-06-20 Released: 2020-07-29 
- Funding Organization(s): Wellcome Trust
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.274 
- R-Value Work: 0.249 
- R-Value Observed: 0.250 
This is version 1.3 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Galactokinase | A, B, C [auth D], D [auth E] | 399 | 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  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P51570 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HFK Query on HFK | F [auth A], H [auth B], K [auth E] | 2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one C20 H22 N4 O2 AZBGHUMVHJKFOO-UHFFFAOYSA-N | |||
S6V (Subject of Investigation/LOI) Query on S6V | I [auth D] | 1-[2-(2-oxidanylidenepyrrolidin-1-yl)ethyl]-3-phenyl-urea C13 H17 N3 O2 OYRHWZOYGOUXNC-UHFFFAOYSA-N | |||
GAL Query on GAL | E [auth A], G [auth B], J [auth E] | beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.274 
- R-Value Work: 0.249 
- R-Value Observed: 0.250 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 73.772 | α = 90 |
b = 114.447 | β = 100.55 |
c = 120.924 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-07-29  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 | Location | Grant Number |
---|---|---|
Wellcome Trust | United Kingdom | 092809/Z/10/Z |
Revision History (Full details and data files)
- Version 1.0: 2020-07-29
Type: Initial release - Version 1.1: 2021-04-07
Changes: Database references - Version 1.2: 2021-04-28
Changes: Database references - Version 1.3: 2024-01-24
Changes: Data collection, Database references, Refinement description