3RDP

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with N-METHYL-FHBT

Structural Biology Knowledgebase: 3RDP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.200

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RDP

Classification: TRANSFERASE

Total Structure Weight: 72307.45

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidine kinase A, B 331 Human herpesvirus 1 EC#: 2.7.1.21 IUBMB
Fragment: UNP RESIDUES 46-376
Gene Name(s): TK UL23

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NMF
Query on NMF

A, B 6-[(2R)-2-(fluoromethyl)-3-hydroxy-propyl]- 1,5-dimethyl-pyrimidine-2,4-dione
C10 H15 F N2 O3
OHXHFKXQCMBBKV-ZETCQYMHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.200
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 114.19 α = 90.00
b = 118.28 β = 90.00
c = 108.87 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-01
  • Released Date: 2011-08-03
  • Deposition author(s): Pernot, L., Perozzo, R., Westermaier, Y., Martic, M., Ametamey, S., Scapozza, L.

Revision History

  • 2013-10-02
    Type: Entry authorship | Details: add author name