3HM8 | pdb_00003hm8

Crystal structure of the C-terminal Hexokinase domain of human HK3

• PDB DOI: https://doi.org/10.2210/pdb3HM8/pdb

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


• Deposited: 2009-05-28 Released: 2009-08-11 
• Deposition Author(s): Nedyalkova, L., Tong, Y., Rabeh, W., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.270 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.245 (Depositor) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the C-terminal Hexokinase domain of human HK3

Nedyalkova, L., Tong, Y., Rabeh, W., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 195.23 kDa 
• Atom Count: 12,633 
• Modeled Residue Count: 1,755 
• Deposited Residue Count: 1,780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexokinase-3	A, B, C, D	445	Homo sapiens	Mutation(s): 0  Gene Names: HK3 EC: 2.7.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P52790 (Homo sapiens) Explore P52790  Go to UniProtKB:  P52790
PHAROS:  P52790 GTEx:  ENSG00000160883

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BG6	F [auth A], H [auth B], J [auth C], L [auth D]	6-O-phosphono-beta-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N
GLC	E [auth A], G [auth B], I [auth C], K [auth D]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.270 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.245 (Depositor) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.904	α = 90
b = 83.904	β = 90
c = 323.327	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Nedyalkova, L., Tong, Y., Rabeh, W., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary