6K76

Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.

• PDB DOI: https://doi.org/10.2210/pdb6K76/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-06 Released: 2020-06-10 
• Deposition Author(s): Koga, Y., Angkawidjaja, C., Matsumura, H., Hokao, R.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.261 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 

Literature

Structural analysis of hexameric structure of glycerol kinase from Thermococcus kodakaraeinsis KOD1

Hokao, R., Matsumura, H., Katsumi, R., Angkawidjaja, C., Takano, K., Kanaya, S., Koga, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 112.95 kDa 
• Atom Count: 7,736 
• Modelled Residue Count: 967 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol kinase	A, B	497	Thermococcus kodakarensis KOD1	Mutation(s): 0  Gene Names: glpK, TK1396 EC: 2.7.1.30
UniProt
Find proteins for O93623 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore O93623  Go to UniProtKB:  O93623

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A], D [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.261 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.862	α = 90
b = 218.862	β = 90
c = 66.244	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Koga, Y., Angkawidjaja, C., Matsumura, H., Hokao, R.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP22780091

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references