Crystal Structure of Human Thymidine Kinase 1

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Structures of thymidine kinase 1 of human and mycoplasmic origin

Welin, M.Kosinska, U.Mikkelsen, N.E.Carnrot, C.Zhu, C.Wang, L.Eriksson, S.Munch-Petersen, B.Eklund, H.

(2004) Proc Natl Acad Sci U S A 101: 17970-17975

  • DOI: https://doi.org/10.1073/pnas.0406332102
  • Primary Citation of Related Structures:  
    1XBT, 2UZ3

  • PubMed Abstract: 

    Cytosolic thymidine kinase 1, TK1, is a well known cell-cycle-regulated enzyme of importance in nucleotide metabolism as well as an activator of antiviral and anticancer drugs such as 3'-azido-3'-deoxythymidine (AZT). We have now determined the structures of the TK1 family, the human and Ureaplasma urealyticum enzymes, in complex with the feedback inhibitor dTTP. The TK1s have a tetrameric structure in which each subunit contains an alpha/beta-domain that is similar to ATPase domains of members of the RecA structural family and a domain containing a structural zinc. The zinc ion connects beta-structures at the root of a beta-ribbon that forms a stem that widens to a lasso-type loop. The thymidine of dTTP is hydrogen-bonded to main-chain atoms predominantly coming from the lasso loop. This binding is in contrast to other deoxyribonucleoside kinases where specific interactions occur with side chains. The TK1 structure differs fundamentally from the structures of the other deoxyribonucleoside kinases, indicating a different evolutionary origin.

  • Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, S-751 24 Uppsala, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidine kinase, cytosolic
A, B, C, D, E
A, B, C, D, E, F, G, H
193Homo sapiensMutation(s): 0 
Gene Names: TK1
UniProt & NIH Common Fund Data Resources
Find proteins for P04183 (Homo sapiens)
Explore P04183 
Go to UniProtKB:  P04183
PHAROS:  P04183
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04183
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TTP

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
K [auth A]
N [auth B]
Q [auth C]
CA [auth G],
FA [auth H],
K [auth A],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
C10 H17 N2 O14 P3
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
I [auth A]
L [auth B]
O [auth C]
AA [auth G],
DA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
Query on MG

Download Ideal Coordinates CCD File 
BA [auth G]
EA [auth H]
J [auth A]
M [auth B]
P [auth C]
BA [auth G],
EA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.672α = 90
b = 123.177β = 130.2
c = 116γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance