1XX6

X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP. Northeast Structural Genomics Target CAR26.

Structural Biology Knowledgebase: 1XX6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.241

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XX6

Classification: TRANSFERASE

Total Structure Weight: 45155.06

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidine kinase A, B 191 Clostridium acetobutylicum EC#: 2.7.1.21 IUBMB
Mutation: M17M, M59M, M118M, M132M, M176M
Gene Name(s): tdk CA_C2887
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B 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, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.241
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.79 α = 90.00
b = 67.17 β = 90.00
c = 103.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-11-04
  • Released Date: 2004-12-21
  • Deposition author(s): Kuzin, A.P., Abashidze, M., Forouhar, F., Vorobiev, S.M., Acton, T.B., Ma, L.-C., Xiao, R., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name