3HPD | pdb_00003hpd

Structure of hydroxyethylthiazole kinase protein from pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb3HPD/pdb
• Entry: 3HPD supersedes: 1V8A

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-04 Released: 2009-06-16 
• Deposition Author(s): Jeyakanthan, J., Thamotharan, S., Kuramitsu, S., Yokoyama, S., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Structure of Hydroxyethylthiazole Kinase Protein from Pyrococcus Horikoshii Ot3

Jeyakanthan, J., Kuramitsu, S., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 29.09 kDa 
• Atom Count: 2,159 
• Modeled Residue Count: 254 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyethylthiazole kinase	A	265	Pyrococcus horikoshii OT3	Mutation(s): 0  EC: 2.7.1.50
UniProt
Find proteins for O58877 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58877  Go to UniProtKB:  O58877

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.242	α = 90
b = 112.242	β = 90
c = 112.242	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Jeyakanthan, J., Thamotharan, S., Kuramitsu, S., Yokoyama, S., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 1V8A

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description