3SUN

RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite 2AP (AT rich sequence)

Structural Biology Knowledgebase: 3SUN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3SUN

Classification: TRANSFERASE / DNA

Total Structure Weight: 113095.52


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 895 Enterobacteria phage rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A, Y567A
Gene Name(s): 43
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(P*CP*(2PR)P*TP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*G)-3' T 16 synthetic template
5'-D(*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*(2DA))-3' P 13 synthetic 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 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
2PR
Query on 2PR
T DNA LINKING C10 H14 N5 O6 P DG
2DA
Query on 2DA
P DNA LINKING C10 H14 N5 O5 P DA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.205
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 74.84 α = 90.00
b = 120.99 β = 90.00
c = 127.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-07-11
  • Released Date: 2011-11-09
  • Deposition author(s): Xia, S., Konigsberg, W.H., Wang, J.

Revision History

  • 2011-11-30
    Type: Citation | Details: Citation update
  • 2011-11-16
    Type: Citation | Details: Citation update