1WKK

Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8

Takeishi, S.Nakagawa, N.Masui, R.Kuramitsu, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
nucleoside diphosphate kinaseA, B137Thermus thermophilusMutation(s): 0 
Gene Names: ndk
EC: 2.7.4.6
UniProt
Find proteins for Q5SLV5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLV5 
Go to UniProtKB:  Q5SLV5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.83α = 90
b = 123.83β = 90
c = 104.302γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance