2B8T

Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine

Structural Biology Knowledgebase: 2B8T SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2B8T

Classification: TRANSFERASE

Total Structure Weight: 103114.19

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidine kinase A, B, C, D 223 Ureaplasma parvum EC#: 2.7.1.21 IUBMB
Mutation: L16F
Gene Name(s): tdk UU594

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

A, B, C, D THYMIDINE
DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE (Synonym)
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

D 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.195
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.16 α = 90.00
b = 115.65 β = 101.02
c = 64.47 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-10
  • Released Date: 2005-12-20
  • Deposition author(s): Kosinska, U., Carnrot, C., Eriksson, S., Wang, L., Eklund, H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4