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 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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
MoleculeChainsSequence LengthOrganismDetailsImage
Uridine-cytidine kinase 2
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
GA [auth E],
I [auth A],
NA [auth F],
P [auth B],
RA [auth G],
GA [auth E],
I [auth A],
NA [auth F],
P [auth B],
RA [auth G],
T [auth C],
TA [auth H],
Y [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
HA [auth E],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
N [auth A],
O [auth A],
OA [auth F],
PA [auth F],
Q [auth B],
QA [auth F],
R [auth B],
S [auth B],
SA [auth G],
U [auth C],
UA [auth H],
V [auth C],
VA [auth H],
W [auth C],
X [auth C],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • 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 



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