2UVQ | pdb_00002uvq

Crystal structure of human uridine-cytidine kinase 1 in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb2UVQ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-13 Released: 2007-03-27 
• Deposition Author(s): Kosinska, U., Stenmark, P., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg Schiavone, L., Hogbom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E.P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Sundstrom, M., Uppenberg, J., Uppsten, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.253 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structure of Human Uridine-Cytidine Kinase 1

Kosinska, U., Stenmark, P., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg Schiavone, L., Hogbom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E.P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Sundstrom, M., Uppenberg, J., Uppsten, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 28.67 kDa 
• Atom Count: 1,734 
• Modeled Residue Count: 211 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URIDINE-CYTIDINE KINASE 1	A	245	Homo sapiens	Mutation(s): 0  EC: 2.7.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HA47 (Homo sapiens) Explore Q9HA47  Go to UniProtKB:  Q9HA47
PHAROS:  Q9HA47 GTEx:  ENSG00000130717

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.253 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.919	α = 90
b = 67.919	β = 90
c = 236.607	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Kosinska, U., Stenmark, P., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg Schiavone, L., Hogbom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E.P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Sundstrom, M., Uppenberg, J., Uppsten, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Nordlund, P.

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description