3E2I

Crystal structure of Thymidine Kinase from S. aureus

Structural Biology Knowledgebase: 3E2I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3E2I

Classification: TRANSFERASE

Total Structure Weight: 24902.68

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidine kinase A 219 Staphylococcus aureus EC#: 2.7.1.21 IUBMB
Gene Name(s): tdk AL077_08825 ASU36_08635 CH51_11455 EQ80_010675 ER12_010660 ERS092844_02291 ERS093009_02316 ERS179246_00399 ERS195423_02067 ERS365775_02415 ERS410449_02287 ERS411009_02499 ERS411017_02570 ERS445051_02075 ERS445052_01282 NI36_10400 RL02_00660 SAFDA_1993 SASCBU26_02125 TM61_09115

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.202
  • Space Group: P 42 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.62 α = 90.00
b = 71.62 β = 90.00
c = 96.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-08-05
  • Released Date: 2009-08-11
  • Deposition author(s): Lam, R., Johns, K., Battaile, K.P., Romanov, V., Lam, K., Pai, E.F., Chirgadze, N.Y.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor