3IH0

Crystal structure of an uncharacterized sugar kinase PH1459 from Pyrococcus horikoshii in complex with AMP-PNP

• PDB DOI: https://doi.org/10.2210/pdb3IH0/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-29 Released: 2009-09-08 
• Deposition Author(s): Kumar, G., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.250 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Crystal structure of an uncharacterized sugar kinase PH1459 from Pyrococcus horikoshii in complex with AMP-PNP

Kumar, G., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

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)

Macromolecule Content

• Total Structure Weight: 70.31 kDa 
• Atom Count: 5,172 
• Modelled Residue Count: 608 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized sugar kinase PH1459	A, B	313	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH1459, PHCC008 EC: 2.7.1
UniProt
Find proteins for O59128 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59128  Go to UniProtKB:  O59128

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GOL	D [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.250 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.17	α = 90
b = 54.07	β = 110.95
c = 77.72	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Kumar, G., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection