3W8R

Mutant structure of Thermus thermophilus HB8 uridine-cytidine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Indispensable residue for uridine binding in the uridine-cytidine kinase family

Tomoike, F.Nakagawa, N.Fukui, K.Yano, T.Kuramitsu, S.Masui, R.

(2017) Biochem Biophys Rep 11: 93-98


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine kinase
A, B
211Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 1 
Gene Names: udk
EC: 2.7.1.48
Find proteins for Q5SKR5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKR5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

Download SDF File 
Download CCD File 
A, B
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
CTN
Query on CTN

Download SDF File 
Download CCD File 
A, B
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
CYTIDINE
C9 H13 N3 O5
UHDGCWIWMRVCDJ-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.300α = 90.00
b = 124.100β = 90.00
c = 60.700γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CNSrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Advisory, Database references, Refinement description