3TY5

Crystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP

Structural Biology Knowledgebase: 3TY5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.178

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3TY5

Classification: TRANSFERASE

Total Structure Weight: 96035.96

Macromolecule Entities
Molecule Chains Length Organism Details
Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase A, B 413 Ruminiclostridium thermocellum EC#: 6.5.1.3 IUBMB
Fragment: Nucleotide Ligase
Mutation: E529G

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

B ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
JSmol
ATP
Query on ATP

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
JSmol
PGE
Query on PGE

B TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.178
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 63.99 α = 90.00
b = 94.38 β = 93.51
c = 75.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-23
  • Released Date: 2012-01-25
  • Deposition author(s): Smith, P., Wang, L., Shuman, S.

Revision History

  • 2012-02-29
    Type: Citation | Details: Citation update
  • 2012-02-22
    Type: Citation | Details: Citation update