3QEP

RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dTTP Opposite Difluorotoluene Nucleoside

Structural Biology Knowledgebase: 3QEP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.167

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QEP

Classification: Transferase / DNA

Total Structure Weight: 114740.98


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 903 Enterobacteria phage rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A, L561A, S565G, Y567A
Gene Name(s): 43
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*CP*GP*(DFT)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') T 18 Synthetic construct DNA Template
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') P 13 Synthetic construct DNA Primer

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

A THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, P CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
DFT
Query on DFT
T DNA LINKING C12 H15 F2 O6 P --
DOC
Query on DOC
P DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.167
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.13 α = 90.00
b = 119.77 β = 90.00
c = 130.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-20
  • Released Date: 2011-08-31
  • Deposition author(s): Xia, S., Konigsberg, W.H., Wang, J.

Revision History

No revisions since initial release