2DXE | pdb_00002dxe

Crystal structure of nucleoside diphosphate kinase in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb2DXE/pdb

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


• Deposited: 2006-08-25 Released: 2007-02-25 
• Deposition Author(s): Kato-Murayama, M., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.190 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of nucleoside diphosphate kinase in complex with GDP

Kato-Murayama, M., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 37.29 kDa 
• Atom Count: 2,904 
• Modeled Residue Count: 310 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B	160	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: ndk EC: 2.7.4.6
UniProt
Find proteins for O58429 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58429  Go to UniProtKB:  O58429

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	F [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
CL	D [auth A], E [auth A], G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.190 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.802	α = 90
b = 69.802	β = 90
c = 107.093	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-25 
Deposition Author(s): Kato-Murayama, M., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-02-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description