5O5Y

Crystal structure of Thermococcus litoralis ADP-dependent glucokinase (GK)

• PDB DOI: https://doi.org/10.2210/pdb5O5Y/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus litoralis DSM 5473
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-02 Released: 2018-10-24 
• Deposition Author(s): Herrera-Morande, A., Castro-Fernandez, V., Merino, F., Ramirez-Sarmiento, C.A., Fernandez, F.J., Guixe, V., Vega, M.C.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness, Spanish National Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.209 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 106.64 kDa 
• Atom Count: 8,059 
• Modelled Residue Count: 903 
• Deposited Residue Count: 928 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-dependent glucokinase,ADP-dependent glucokinase,ADP-dependent glucokinase	A, B	464	Thermococcus litoralis DSM 5473	Mutation(s): 0  Gene Names: glkA, OCC_09701 EC: 2.7.1.147
UniProt
Find proteins for Q7M537 (Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C)) Explore Q7M537  Go to UniProtKB:  Q7M537

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	N [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
PGE	J [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.209 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.64	α = 90
b = 97.61	β = 90
c = 113.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
AMoRE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Herrera-Morande, A., Castro-Fernandez, V., Merino, F., Ramirez-Sarmiento, C.A., Fernandez, F.J., Guixe, V., Vega, M.C.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2015-66206-C2-2-R
Spanish National Research Council	Spain	PIE-201620E064

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary