2A2C

x-ray structure of human N-acetyl galactosamine kinase complexed with Mg-ADP and N-acetyl galactosamine 1-phosphate

• PDB DOI: https://doi.org/10.2210/pdb2A2C/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-22 Released: 2005-07-26 
• Deposition Author(s): Thoden, J.B., Holden, H.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.201 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.6 kDa 
• Atom Count: 3,976 
• Modelled Residue Count: 446 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylgalactosamine kinase	A	478	Homo sapiens	Mutation(s): 0  Gene Names: GALK2, GK2 EC: 2.7.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q01415 (Homo sapiens) Explore Q01415  Go to UniProtKB:  Q01415
PHAROS:  Q01415 GTEx:  ENSG00000156958

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	F [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
NG1	B [auth A]	2-acetamido-2-deoxy-1-O-phosphono-alpha-D-galactopyranose C8 H16 N O9 P FZLJPEPAYPUMMR-JAJWTYFOSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.201 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.8	α = 90
b = 123.8	β = 90
c = 60.1	γ = 120

Software Package:

Software Name	Purpose
dSTAR	data collection
HKL-2000	data reduction
SOLVE	phasing
TNT	refinement
d*TREK	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Thoden, J.B., Holden, H.M.

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-13
  Changes: Database references, Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Structure summary