3KTQ

CRYSTAL STRUCTURE OF AN ACTIVE TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS

Structural Biology Knowledgebase: 3KTQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.218

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3KTQ

Classification: TRANSFERASE / DNA

Total Structure Weight: 69392.61


Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (LARGE FRAGMENT OF DNA POLYMERASE I) A 540 Thermus aquaticus EC#: 2.7.7.7 IUBMB
Gene Name(s): polA pol1
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)-3') B 12 synthetic
DNA (5'-D(*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') C 14 synthetic COMPLEXED WITH 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE

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

A 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
DOC
Query on DOC
B DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.218
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 108.03 α = 90.00
b = 108.03 β = 90.00
c = 90.17 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-07-28
  • Released Date: 1999-01-13
  • Deposition author(s): Li, Y., Waksman, G.

Revision History

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