6PWZ

Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.254 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P6DClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Incorporation of novel azido-nucleotides into RNA

Nainar, S.Cuthbert, B.J.Goulding, C.W.Spitale, R.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine-cytidine kinase 2
A, B, C, D, E
250Homo sapiensMutation(s): 0 
Gene Names: UCK2UMPK
EC: 2.7.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZX2 (Homo sapiens)
Explore Q9BZX2 
Go to UniProtKB:  Q9BZX2
PHAROS:  Q9BZX2
GTEx:  ENSG00000143179 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZX2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6D (Subject of Investigation/LOI)
Query on P6D

Download Ideal Coordinates CCD File 
FA [auth D],
MA [auth E],
WA [auth H]
2'-azidocytidine
C9 H13 N6 O4
SXKUZFQHWHCRFO-XVFCMESISA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
GA [auth E]
I [auth A]
NA [auth F]
P [auth B]
RA [auth G]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.73α = 90
b = 84.74β = 95.36
c = 153.579γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P6DClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United States1R21MH113062

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description