9K6K | pdb_00009k6k

monkeypox thymidine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 
    0.264 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural and mechanistic insight into the phosphorylation reaction catalyzed by mpox virus thymidine kinase.

Zhang, T.Chen, X.Tao, C.Huang, H.Luo, Z.Liu, M.Cui, W.Wang, W.

(2025) Antiviral Res 237: 106125-106125

  • DOI: https://doi.org/10.1016/j.antiviral.2025.106125
  • Primary Citation Related Structures: 
    9K6K

  • PubMed Abstract: 

    Mpox virus (MPXV) is the etiological agent of mpox, which is a major threat to human health. The identification of potential drug targets and the development of effective antiviral therapies are still urgently needed. The thymidine kinase (TK) encoded by MPXV initiates the deoxythymidine triphosphate (dTTP) salvage synthesis pathway and facilitates viral DNA replication. MPXV without TK presents significant replication defects. MPXV TK is also responsible for the activation of nucleos(t)ide analogs, which are an important class of antivirals. Despite its importance in the viral life cycle and antiviral development, the structure and catalytic mechanism of MPXV TK are not fully understood. Here, we determined the three-dimensional structure of an MPXV TK variant, in which the glutamic acid at position 83 was substituted with alanine. MPXV TK consists of two domains and forms a tetramer. One protomer binds dTTP with two lassos and a P-loop, while the other protomers are captured in apo-form. Mutation of residues near the dTTP-binding site significantly reduces the catalytic activity of MPXV TK, indicating the importance of these residues in substrate binding and/or catalysis. Specifically, E83 is found to play a crucial role in stabilizing dTTP and lasso II. A biochemical assay confirmed that dTTP functions as a feedback inhibitor of MPXV TK and its inhibitory potency was evaluated. These results may facilitate the discovery of specific inhibitors targeting TK to mitigate MPXV infections.


  • Organizational Affiliation
    • College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China.

Macromolecule Content 

  • Total Structure Weight: 81.11 kDa 
  • Atom Count: 4,554 
  • Modeled Residue Count: 590 
  • Deposited Residue Count: 708 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thymidine kinase
A, B, C, D
177Monkeypox virusMutation(s): 1 
Gene Names: OPG101TKMPXV084
EC: 2.7.1.21
UniProt
Find proteins for A0A7H0DN73 (Monkeypox virus)
Explore A0A7H0DN73 
Go to UniProtKB:  A0A7H0DN73
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7H0DN73
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TTP
(Subject of Investigation/LOI)

Query on TTP



Download:Ideal Coordinates CCD File
G [auth B]THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
PO4
(Subject of Investigation/LOI)

Query on PO4



Download:Ideal Coordinates CCD File
F [auth A],
J [auth C],
L [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
I [auth C],
K [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free:  0.264 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.272α = 90
b = 63.762β = 111.16
c = 117.106γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaKJQN202300442

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release